test_that("use", {
check_empty_beautier_folder()
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()))
expect_true(is_site_model(create_gtr_site_model()))
expect_false(is_site_model(NA))
expect_false(is_site_model(NULL))
expect_false(is_site_model("nonsense"))
expect_false(is_site_model(list(name = "nonsense")))
expect_false(is_site_model(list(name = "JC69")))
expect_false(is_gtr_site_model(NA))
expect_false(is_gtr_site_model(NULL))
expect_false(is_gtr_site_model("nonsense"))
expect_false(is_hky_site_model(NA))
expect_false(is_hky_site_model(NULL))
expect_false(is_hky_site_model("nonsense"))
expect_false(is_jc69_site_model(NA))
expect_false(is_jc69_site_model(NULL))
expect_false(is_jc69_site_model("nonsense"))
expect_false(is_tn93_site_model(NA))
expect_false(is_tn93_site_model(NULL))
expect_false(is_tn93_site_model("nonsense"))
})
test_that("is_site_model: devious", {
g <- create_jc69_site_model()
expect_true(is_site_model(g))
# No 'name'
h <- g[names(g) != "name"]
expect_false(is_site_model(h))
# Invald 'name'
h <- g
h$name <- "nonsense"
expect_false(is_site_model(h))
# No 'id'
h <- g[names(g) != "id"]
expect_false(is_site_model(h))
# No 'gamma_site_model'
h <- g[names(g) != "gamma_site_model"]
expect_false(is_site_model(h))
# Invalid 'gamma_site_model'
h <- g
h$gamma_site_model <- "nonsense"
expect_false(is_site_model(h))
})
test_that("is_gtr_site_model: devious", {
g <- create_gtr_site_model()
expect_true(is_gtr_site_model(g))
# No site model
h <- g
h <- "nonsense"
expect_false(is_gtr_site_model(h))
# Invalid name
h <- g
h$name <- "nonsense"
expect_false(is_gtr_site_model(h))
# No 'rate_ac_prior_distr'
h <- g[names(g) != "rate_ac_prior_distr"]
expect_false(is_gtr_site_model(h))
# No 'rate_ag_prior_distr'
h <- g[names(g) != "rate_ag_prior_distr"]
expect_false(is_gtr_site_model(h))
# No 'rate_at_prior_distr'
h <- g[names(g) != "rate_at_prior_distr"]
expect_false(is_gtr_site_model(h))
# No 'rate_cg_prior_distr'
h <- g[names(g) != "rate_cg_prior_distr"]
expect_false(is_gtr_site_model(h))
# No 'rate_gt_prior_distr'
h <- g[names(g) != "rate_gt_prior_distr"]
expect_false(is_gtr_site_model(h))
# No 'rate_ac_param'
h <- g[names(g) != "rate_ac_param"]
expect_false(is_gtr_site_model(h))
# No 'rate_ag_param'
h <- g[names(g) != "rate_ag_param"]
expect_false(is_gtr_site_model(h))
# No 'rate_at_param'
h <- g[names(g) != "rate_at_param"]
expect_false(is_gtr_site_model(h))
# No 'rate_cg_param'
h <- g[names(g) != "rate_cg_param"]
expect_false(is_gtr_site_model(h))
# No 'rate_ct_param'
h <- g[names(g) != "rate_ct_param"]
expect_false(is_gtr_site_model(h))
# No 'rate_gt_param'
h <- g[names(g) != "rate_gt_param"]
expect_false(is_gtr_site_model(h))
# No 'freq_equilibrium'
h <- g[names(g) != "freq_equilibrium"]
expect_false(is_gtr_site_model(h))
# Invalid distributions
h <- g
h$rate_ac_prior_distr <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_ag_prior_distr <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_at_prior_distr <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_cg_prior_distr <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_gt_prior_distr <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_ac_param <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_ag_param <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_at_param <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_cg_param <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_ct_param <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$rate_gt_param <- "nonsense"
expect_false(is_gtr_site_model(h))
h <- g
h$freq_equilibrium <- "nonsense"
expect_false(is_gtr_site_model(h))
})
test_that("is_hky_site_model: devious", {
g <- create_hky_site_model()
expect_true(is_hky_site_model(g))
# No site model
h <- g
h <- "nonsense"
expect_false(is_hky_site_model(h))
# Invalid name
h <- g
h$name <- "nonsense"
expect_false(is_hky_site_model(h))
# No 'kappa_param'
h <- g[names(g) != "kappa_param"]
expect_false(is_hky_site_model(h))
# No 'kappa_prior_distr'
h <- g[names(g) != "kappa_prior_distr"]
expect_false(is_hky_site_model(h))
# Invalid 'kappa_prior_distr'
h <- g
h$kappa_prior_distr <- "nonsense"
expect_false(is_hky_site_model(h))
# No 'freq_equilibrium'
h <- g[names(g) != "freq_equilibrium"]
expect_false(is_hky_site_model(h))
# Invalid 'freq_equilibrium'
h <- g
h$freq_equilibrium <- "nonsense"
expect_false(is_hky_site_model(h))
})
test_that("is_tn93_site_model: devious", {
g <- create_tn93_site_model()
expect_true(is_tn93_site_model(g))
# No site model
h <- g
h <- "nonsense"
expect_false(is_tn93_site_model(h))
# Invalid name
h <- g
h$name <- "nonsense"
expect_false(is_tn93_site_model(h))
# No 'kappa_1_prior_distr'
h <- g[names(g) != "kappa_1_prior_distr"]
expect_false(is_tn93_site_model(h))
# Invalid 'kappa_1_prior_distr'
h <- g
h$kappa_1_prior_distr <- "nonsense"
expect_false(is_tn93_site_model(h))
# No 'kappa_2_prior_distr'
h <- g[names(g) != "kappa_2_prior_distr"]
expect_false(is_tn93_site_model(h))
# Invalid 'kappa_2_prior_distr'
h <- g
h$kappa_2_prior_distr <- "nonsense"
expect_false(is_tn93_site_model(h))
# No 'kappa_1_param'
h <- g[names(g) != "kappa_1_param"]
expect_false(is_tn93_site_model(h))
# Invalid 'kappa_1_param'
h <- g
h$kappa_1_param <- "nonsense"
expect_false(is_tn93_site_model(h))
# No 'kappa_2_param'
h <- g[names(g) != "kappa_2_param"]
expect_false(is_tn93_site_model(h))
# Ivalid 'kappa_2_param'
h <- g
h$kappa_2_param <- "nonsense"
expect_false(is_tn93_site_model(h))
# No 'freq_equilibrium'
h <- g[names(g) != "freq_equilibrium"]
expect_false(is_tn93_site_model(h))
# Invalid 'freq_equilibrium'
h <- g
h$freq_equilibrium <- "nonsense"
expect_false(is_tn93_site_model(h))
})
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