context("is_init_site_model")
test_that("is_init_site_model", {
expect_false(is_init_site_model("nonsense"))
expect_false(is_init_gtr_site_model("nonsense"))
})
test_that("is_init_gtr_site_model", {
g <- create_gtr_site_model(
id = 42,
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape_prior_distr = create_one_div_x_distr(id = 0)
),
rate_ac_prior_distr = create_one_div_x_distr(id = 1),
rate_ag_prior_distr = create_one_div_x_distr(id = 2),
rate_at_prior_distr = create_one_div_x_distr(id = 3),
rate_cg_prior_distr = create_one_div_x_distr(id = 4),
rate_gt_prior_distr = create_one_div_x_distr(id = 6),
rate_ac_param = create_rate_ac_param(id = 7),
rate_ag_param = create_rate_ac_param(id = 8),
rate_at_param = create_rate_ac_param(id = 9),
rate_cg_param = create_rate_ac_param(id = 10),
rate_ct_param = create_rate_ac_param(id = 11),
rate_gt_param = create_rate_ac_param(id = 12)
)
expect_true(is_init_gtr_site_model(g))
# Uninitialize 'rate_ac_prior_distr'
h <- g
h$rate_ac_prior_distr$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'rate_ag_prior_distr'
h <- g
h$rate_ag_prior_distr$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'rate_at_prior_distr'
h <- g
h$rate_at_prior_distr$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'rate_cg_prior_distr'
h <- g
h$rate_cg_prior_distr$id <- NA
expect_false(is_init_gtr_site_model(h))
# No 'rate_cg_prior_distr' yet
# Uninitialize 'rate_gt_prior_distr'
h <- g
h$rate_gt_prior_distr$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'rate_ac_param'
h <- g
h$rate_ac_param$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'rate_ag_param'
h <- g
h$rate_ag_param$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'rate_at_param'
h <- g
h$rate_at_param$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'rate_cg_param'
h <- g
h$rate_cg_param$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'rate_ct_param'
h <- g
h$rate_ct_param$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'rate_gt_param'
h <- g
h$rate_gt_param$id <- NA
expect_false(is_init_gtr_site_model(h))
# Uninitialize 'gamma_site_model'
h <- g
h$gamma_site_model$gamma_shape_prior_distr$id <- NA
expect_false(is_init_gtr_site_model(h))
})
test_that("is_init_site_model on HKY site model", {
expect_true(
is_init_site_model(
create_hky_site_model(
kappa_prior_distr = create_log_normal_distr(id = 1,
m = create_m_param(id = 1),
s = create_s_param(id = 2)
),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape_prior_distr = create_one_div_x_distr(id = 3)
)
)
)
)
expect_false(
is_init_site_model(
create_hky_site_model(
kappa_prior_distr = create_log_normal_distr(
id = NA,
m = create_m_param(id = 1),
s = create_s_param(id = 2)
),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape_prior_distr = create_one_div_x_distr(id = 3)
)
)
)
)
expect_false(
is_init_site_model(
create_hky_site_model(
kappa_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = NA),
s = create_s_param(id = 2)
),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape_prior_distr = create_one_div_x_distr(id = 3)
)
)
)
)
expect_false(
is_init_site_model(
create_hky_site_model(
kappa_prior_distr = create_log_normal_distr(
id = 1,
m = create_m_param(id = 1),
s = create_s_param(id = NA)
),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape_prior_distr = create_one_div_x_distr(id = 3)
)
)
)
)
expect_false(
is_init_site_model(
create_hky_site_model(
kappa_prior_distr = create_log_normal_distr(id = 1,
m = create_m_param(id = 1),
s = create_s_param(id = 2)
),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape_prior_distr = create_one_div_x_distr(id = NA)
)
)
)
)
})
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