test_that("simulate_outbreak", {
inf_params <- c("beta_0" = -2, "beta_1" = 1)
smear_pos_prob <- .8
max_size <- 30
K <- 5
out <- simulate_outbreak(K = K,
inf_params = inf_params,
smear_pos_prob = smear_pos_prob,
max_size = max_size)
expect_equal(length(unique(out$cluster_id)), K)
#################
##Start at an outsider
#################
start_at_outsider <- TRUE
inf_params <- c("beta_0" = -2, "beta_1" = 1.5)
smear_pos_prob <- .5
max_size <- 10
K <- 10
out <- simulate_outbreak(K = K,
inf_params = inf_params,
smear_pos_prob = smear_pos_prob,
max_size = max_size,
start_at_outsider = start_at_outsider)
expect_true(length(unique(out$cluster_id)) <= K)
## ###############
start_at_outsider <- TRUE
keep_zero_clusters <- TRUE
inf_params <- c("beta_0" = -2, "beta_1" = 1.5)
smear_pos_prob <- .5
max_size <- 10
K <- 10
out <- simulate_outbreak(K = K,
inf_params = inf_params,
smear_pos_prob = smear_pos_prob,
max_size = max_size,
start_at_outsider = start_at_outsider,
keep_zero_clusters = keep_zero_clusters)
expect_true(length(unique(out$cluster_id)) == K)
})
test_that("move_up_gen", {
id <- c("C1-G1-N1",
"C1-G2-N1")
out <- move_up_gen(id)
exp_out <- c("C1-G0-N1",
"C1-G1-N1")
expect_equal(out, exp_out)
#############
id <- c("C1-G1-N1",
NA)
out <- move_up_gen(id)
exp_out <- c("C1-G0-N1",
NA)
expect_equal(out, exp_out)
})
test_that("format_to_outsider", {
df <- data.frame(cluster_id = c(1, 1),
person_id = c("C1-G1-N1",
"C1-G2-N1"),
smear = c(1, -1),
gen = c(1, 2),
inf_id = c(NA, "C1-G1-N1"),
n_inf = c(1, 0),
cluster_size = c(2, 2),
cluster_pos = c(1, 1),
censored = FALSE,
stringsAsFactors = FALSE)
exp_out <- data.frame(cluster_id = c(1),
person_id = c("C1-G2-N1"),
smear = c(-1),
gen = c(1),
inf_id = c(NA),
n_inf = c(0),
cluster_size = c(1),
cluster_pos = c(0),
censored = FALSE,
stringsAsFactors = FALSE)
out <- format_to_outsider(df)
expect_equal(out$cluster_pos, exp_out$cluster_pos)
expect_equal(out$cluster_size, exp_out$cluster_size)
#####################################################
df <- data.frame(cluster_id = c(1, 1, 2, 2, 2, 2),
person_id = c("C1-G1-N1",
"C1-G2-N1",
"C2-G1-N1",
"C2-G2-N1",
"C2-G2-N2",
"C2-G3-N1"),
smear = c(1, -1,
1, 1, -1, 1),
gen = c(1, 2,
1, 2, 2, 3),
inf_id = c(NA, "C1-G1-N1",
NA, "C2-G1-N1", "C2-G1-N1", "C2-G2-N2"),
n_inf = c(1, 0,
2, 0, 1, 0),
cluster_size = c(2, 2,
4, 4, 4, 4),
cluster_pos = c(1, 1,
3, 3, 3, 3),
censored = FALSE,
stringsAsFactors = FALSE)
exp_out <- data.frame(cluster_id = c(1, 2, 2, 2),
person_id = c("C1-G1-N1",
"C2-G1-N1",
"C2-G1-N2",
"C2-G2-N1"),
smear = c(-1,
1, -1, 1),
gen = c(1,
1, 1, 2),
inf_id = c(NA,
NA, NA, "C2-G1-N2"),
n_inf = c(0,
0, 1, 0),
cluster_size = c(1,
3, 3, 3),
cluster_pos = c(0,
2, 2, 2),
censored = FALSE,
stringsAsFactors = FALSE)
out <- format_to_outsider(df)
expect_equal(out$cluster_pos, exp_out$cluster_pos)
expect_equal(out$cluster_size, exp_out$cluster_size)
################################################3
df <- data.frame(cluster_id = c(1, 2),
person_id = c("C1-G1-N1",
"C2-G1-N1"),
smear = c(1, -1),
gen = c(1, 1),
inf_id = c(NA, NA),
n_inf = c(0, 0),
cluster_size = c(1, 1),
cluster_pos = c(0, 0),
censored = FALSE,
stringsAsFactors = FALSE)
exp_out <- data.frame(cluster_id = c(1, 2),
person_id = c("C1-G0-N1",
"C2-G0-N1"),
smear = c(1,
-1),
gen = c(0, 0),
inf_id = as.character(c(NA,
NA)),
n_inf = c(0,
0),
cluster_size = c(0,
0),
cluster_pos = as.integer(c(1,
0)),
censored = FALSE,
stringsAsFactors = FALSE)
out <- format_to_outsider(df,
keep_zero_clusters = TRUE)
expect_equal(out$gen, exp_out$gen)
######################33
df <- data.frame(cluster_id = c(1, 2, 2),
person_id = c("C1-G1-N1",
"C2-G1-N1",
"C2-G2-N1"),
smear = c(1, -1, -1),
gen = c(1, 1, 2),
inf_id = c(NA, NA, "C2-G1-N1"),
n_inf = c(0, 1, 0),
cluster_size = c(1, 2, 2),
cluster_pos = c(1, 0, 0),
censored = FALSE,
stringsAsFactors = FALSE)
exp_out <- data.frame(cluster_id = c(1, 2),
person_id = c("C1-G0-N1",
"C2-G1-N1"),
smear = c(1,
-1),
gen = c(0, 1),
inf_id = as.character(c(NA,
NA)),
n_inf = c(0,
0),
cluster_size = c(0,
1),
cluster_pos = as.integer(c(1,
0)),
censored = FALSE,
stringsAsFactors = FALSE)
out <- format_to_outsider(df,
keep_zero_clusters = TRUE)
expect_equal(out$gen, exp_out$gen)
})
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