Nothing

```
context("unphased")
test_that("unphased, use", {
testthat::skip_on_os("solaris")
population_size <- 100
max_t <- 110
vx <- sim_phased_unphased(pop_size = population_size,
freq_ancestor_1 = 0.5,
total_runtime = max_t,
size_in_morgan = 1,
markers = 1000,
time_points = c(50, 100))
num_indiv <- length(unique(vx$individual))
testthat::expect_equal(num_indiv, 10)
testthat::expect_equal(length(unique(vx$time)), 2)
local_data <- subset(vx, vx$individual == 0 &
vx$time == 100)
ll_100 <- log_likelihood_diploid(cbind(1,
local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
pop_size = 100,
freq_ancestor_1 = 0.5,
t = 100,
phased = FALSE)
ll_2000 <- log_likelihood_diploid(cbind(1,
local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
pop_size = 100,
freq_ancestor_1 = 0.5,
phased = FALSE,
t = 2000)
testthat::expect_gte(ll_100, ll_2000)
vx <- sim_phased_unphased(pop_size = 10000,
freq_ancestor_1 = 0.1,
total_runtime = 20,
size_in_morgan = 1,
markers = 10000,
time_points = c(20))
local_data <- subset(vx, vx$individual == 0 &
vx$time == 20)
ll_30 <- log_likelihood_diploid(cbind(1, local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
pop_size = 1000,
freq_ancestor_1 = 0.1,
phased = FALSE,
t = 30)
ll_100 <- log_likelihood_diploid(cbind(1, local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
pop_size = 1000,
freq_ancestor_1 = 0.1,
phased = FALSE,
t = 600)
testthat::expect_gte(ll_30, ll_100)
multi_ll <- log_likelihood_diploid(cbind(1,
local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
pop_size = 1000,
freq_ancestor_1 = 0.1,
phased = FALSE,
t = c(3, 30000))
testthat::expect_true(length(multi_ll) == 2)
testthat::expect_gt(multi_ll[1], multi_ll[2])
})
test_that("unphased, time points", {
testthat::skip_on_os("solaris")
population_size <- 100
max_t <- 10
vx <- sim_phased_unphased(pop_size = population_size,
freq_ancestor_1 = 0.5,
total_runtime = max_t,
size_in_morgan = 1,
markers = 1000,
time_points = -1)
sim_t <- unique(vx$time)
testthat::expect_equal(length(sim_t), max_t + 1) # [0, 1, ..., max_t]
testthat::expect_warning(
vx <- sim_phased_unphased(pop_size = population_size,
freq_ancestor_1 = 0.5,
total_runtime = max_t,
size_in_morgan = 1,
markers = 1000,
time_points = max_t + 5)
)
testthat::expect_equal(length(unique(vx$time)), 1)
})
test_that("unphased, junctions", {
testthat::skip_on_os("solaris")
N <- 10000 # nolint
R <- 10000 # nolint
t <- 10
H_0 <- 0.5 # nolint
C <- 1 # nolint
testthat::expect_output(
vx <- sim_phased_unphased(pop_size = N,
freq_ancestor_1 = H_0,
total_runtime = t,
size_in_morgan = C,
markers = R,
time_points = t,
num_indiv_sampled = 100,
record_true_junctions = TRUE,
verbose = TRUE)
)
num_j_true <- mean(c(vx$true_results$junctions_chrom_1,
vx$true_results$junctions_chrom_2))
vx <- vx$results
num_j <- c()
for (i in unique(vx$individual)) {
dd <- subset(vx, vx$individual == i)
num_j_1 <- sum(abs(diff(dd$anc_chrom_1)))
num_j_2 <- sum(abs(diff(dd$anc_chrom_1)))
num_j <- c(num_j, c(num_j_1, num_j_2))
}
obs_j <- mean(num_j)
exp_j <- junctions::number_of_junctions(N = N,
R = R,
H_0 = H_0,
C = C,
t = t)
testthat::expect_equal(obs_j, exp_j, tolerance = 0.2)
N <- 10000 # nolint
R <- 10000 # nolint
t <- 20
H_0 <- 0.5 # nolint
C <- 1 # nolint
vx <- sim_phased_unphased(pop_size = N,
freq_ancestor_1 = H_0,
total_runtime = t,
size_in_morgan = C,
markers = R,
time_points = t,
num_indiv_sampled = 30)
num_j <- c()
for (i in unique(vx$individual)) {
dd <- subset(vx, vx$individual == i)
num_j_1 <- sum(abs(diff(dd$anc_chrom_1)))
num_j_2 <- sum(abs(diff(dd$anc_chrom_1)))
num_j <- c(num_j, c(num_j_1, num_j_2))
}
obs_j <- mean(num_j)
exp_j <- junctions::number_of_junctions(N = N,
R = R,
H_0 = H_0,
C = C,
t = t)
testthat::expect_equal(obs_j, exp_j, tolerance = 0.2)
})
```

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