test_that("use, default arguments", {
# English
expect_true(is_site_model(create_gtr_site_model()))
expect_true(is_site_model(create_jc69_site_model()))
expect_true(is_site_model(create_hky_site_model()))
expect_true(is_site_model(create_tn93_site_model()))
# Search-tree friendly
expect_true(is_site_model(create_site_model_gtr()))
expect_true(is_site_model(create_site_model_jc69()))
expect_true(is_site_model(create_site_model_hky()))
expect_true(is_site_model(create_site_model_tn93()))
})
test_that("abuse", {
expect_error(
create_site_model(
name = "nonsense",
id = "OK"
),
"'site model' must be a site model name, which is one of these: "
)
expect_error(
create_site_model(
name = "JC69",
id = "OK",
gamma_site_model = "nonsense"
),
"'gamma_cat_count' must be an element of a 'gamma_site_model'"
)
})
test_that("create_gtr_site_model: new interface", {
# Old interface
expect_silent(
create_gtr_site_model(
rate_ac_param = create_rate_ac_param(value = 1.2),
rate_ag_param = create_rate_ag_param(value = 2.3),
rate_at_param = create_rate_at_param(value = 3.4),
rate_cg_param = create_rate_cg_param(value = 4.5),
rate_ct_param = create_rate_ct_param(value = 5.6),
rate_gt_param = create_rate_gt_param(value = 6.7)
)
)
# New interface
expect_silent(
create_gtr_site_model(
rate_ac_param = 1.2,
rate_ag_param = 2.3,
rate_at_param = 3.4,
rate_cg_param = 4.5,
rate_ct_param = 5.6,
rate_gt_param = 6.7
)
)
})
test_that("create_tn93_site_model: new interface", {
# Old interface
expect_silent(
create_tn93_site_model(
kappa_1_param = create_kappa_1_param(value = 1.2),
kappa_2_param = create_kappa_1_param(value = 2.3)
)
)
# New interface
expect_silent(
create_tn93_site_model(
kappa_1_param = 1.2,
kappa_2_param = 2.3
)
)
})
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