Nothing

```
context("phased")
test_that("phased, use", {
testthat::skip_on_os("solaris")
vx <- sim_phased_unphased(pop_size = 100,
freq_ancestor_1 = 0.5,
total_runtime = 120,
size_in_morgan = 1,
markers = 1000,
time_points = c(100, 120))
num_indiv <- length(unique(vx$individual))
testthat::expect_equal(num_indiv, 10)
testthat::expect_equal(length(unique(vx$time)), 2)
found <- c()
focal_time <- 100
for (indiv in 0:9) {
local_data <- subset(vx, vx$individual == indiv &
vx$time == focal_time)
estim_time <- estimate_time_diploid(cbind(1, 1,
local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
phased = TRUE,
pop_size = 100,
freq_ancestor_1 = 0.5,
upper_lim = 200)
found[indiv + 1] <- estim_time$time[[1]]
}
testthat::expect_equal(mean(found), focal_time, tolerance = 10)
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$anc_chrom_2),
phased = TRUE,
pop_size = 100,
freq_ancestor_1 = 0.5,
t = 100)
ll_2000 <- log_likelihood_diploid(cbind(1,
local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
phased = TRUE,
pop_size = 100,
freq_ancestor_1 = 0.5,
t = 2000)
testthat::expect_gte(ll_100, ll_2000)
vx <- sim_phased_unphased(pop_size = 1000,
freq_ancestor_1 = 0.1,
total_runtime = 30,
size_in_morgan = 1,
markers = 1000,
time_points = c(30))
local_data <- subset(vx, vx$individual == 0 &
vx$time == 30)
ll_30 <- log_likelihood_diploid(cbind(1,
local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
phased = TRUE,
pop_size = 1000,
freq_ancestor_1 = 0.1,
t = 30)
ll_900 <- log_likelihood_diploid(cbind(1,
local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
phased = TRUE,
pop_size = 1000,
freq_ancestor_1 = 0.1,
t = 900)
testthat::expect_gte(ll_30, ll_900)
multi_ll <- log_likelihood_diploid(cbind(1,
local_data$location,
local_data$anc_chrom_1,
local_data$anc_chrom_2),
phased = TRUE,
pop_size = 1000,
freq_ancestor_1 = 0.1,
t = c(30, 100, 300))
testthat::expect_true(length(multi_ll) == 3)
})
test_that("phased, expectation", {
testthat::skip_on_os("solaris")
vx <- sim_phased_unphased(pop_size = 10000,
freq_ancestor_1 = 0.5,
total_runtime = 100,
size_in_morgan = 1,
time_points = c(20),
record_true_junctions = TRUE)
a <- mean(c(vx$true_results$junctions_chrom_1,
vx$true_results$junctions_chrom_2))
expected_j <- number_of_junctions(N = 10000, t = 20)
testthat::expect_true(abs(a - expected_j) / expected_j < 0.5)
})
```

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