context("site_models_to_xml_state")
test_that("JC69 JC69 JC69 JC69", {
expected <- c(
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_jc69_site_model(id = "anthus_aco"),
create_jc69_site_model(id = "anthus_nd2"),
create_jc69_site_model(id = "anthus_nd3"),
create_jc69_site_model(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("HKY HKY HKY HKY", {
expected <- c(
"<parameter id=\"kappa.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_aco\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_nd2\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_nd3\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_nd4\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>" # nolint XML can be long
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_hky_site_model(id = "anthus_aco"),
create_hky_site_model(id = "anthus_nd2"),
create_hky_site_model(id = "anthus_nd3"),
create_hky_site_model(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("TN93 TN93 TN93 TN93", {
expected <- c(
"<parameter id=\"kappa1.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa2.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa1.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa2.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa1.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa2.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa1.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"kappa2.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_aco\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_nd2\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_nd3\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_nd4\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>" # nolint XML can be long
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_tn93_site_model(id = "anthus_aco"),
create_tn93_site_model(id = "anthus_nd2"),
create_tn93_site_model(id = "anthus_nd3"),
create_tn93_site_model(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("GTR GTR GTR GTR", {
expected <- c(
"<parameter id=\"rateAC.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAG.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAT.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateCG.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateGT.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAC.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAG.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAT.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateCG.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateGT.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAC.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAG.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAT.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateCG.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateGT.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAC.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAG.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateAT.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateCG.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"rateGT.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_aco\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_nd2\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_nd3\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML can be long
"<parameter id=\"freqParameter.s:anthus_nd4\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>" # nolint XML can be long
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_gtr_site_model(id = "anthus_aco"),
create_gtr_site_model(id = "anthus_nd2"),
create_gtr_site_model(id = "anthus_nd3"),
create_gtr_site_model(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("HKY 0 HKY 1 HKY 2 HKY 3 GCC", {
expected <- c(
"<parameter id=\"kappa.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"kappa.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"kappa.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"kappa.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd3\" name=\"stateNode\">1.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd4\" name=\"stateNode\">1.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"freqParameter.s:anthus_aco\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"freqParameter.s:anthus_nd2\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"freqParameter.s:anthus_nd3\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"freqParameter.s:anthus_nd4\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>" # nolint XML is long, so this line is long
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_hky_site_model(id = "anthus_aco",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 0)),
create_hky_site_model(id = "anthus_nd2",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 1)),
create_hky_site_model(id = "anthus_nd3",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 2)),
create_hky_site_model(id = "anthus_nd4",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 3))
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("JC69 1 JC69 1 JC69 1 JC69 1 GCC", {
expected <- c(
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_jc69_site_model(id = "anthus_aco",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 1)
),
create_jc69_site_model(id = "anthus_nd2",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 1)
),
create_jc69_site_model(id = "anthus_nd3",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 1)
),
create_jc69_site_model(id = "anthus_nd4",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 1)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("JC69 2 JC69 2 JC69 2 JC69 2 GCC", {
expected <- c(
"<parameter id=\"gammaShape.s:anthus_aco\" name=\"stateNode\">1.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd2\" name=\"stateNode\">1.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd3\" name=\"stateNode\">1.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd4\" name=\"stateNode\">1.0</parameter>" # nolint XML is long, so this line is long
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_jc69_site_model(id = "anthus_aco",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 2)
),
create_jc69_site_model(id = "anthus_nd2",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 2)
),
create_jc69_site_model(id = "anthus_nd3",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 2)
),
create_jc69_site_model(id = "anthus_nd4",
gamma_site_model = create_gamma_site_model(gamma_cat_count = 2)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("JC69 2 JC69 2 JC69 2 JC69 2 GCC diff shapes diff prop_inv", {
expected <- c(
"<parameter id=\"gammaShape.s:anthus_aco\" name=\"stateNode\">1.1</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd2\" name=\"stateNode\">1.2</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd3\" name=\"stateNode\">1.3</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd4\" name=\"stateNode\">1.4</parameter>" # nolint XML is long, so this line is long
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_jc69_site_model(id = "anthus_aco",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2, gamma_shape = "1.1", prop_invariant = 0.1)
),
create_jc69_site_model(id = "anthus_nd2",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2, gamma_shape = "1.2", prop_invariant = 0.2)
),
create_jc69_site_model(id = "anthus_nd3",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2, gamma_shape = "1.3", prop_invariant = 0.3)
),
create_jc69_site_model(id = "anthus_nd4",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2, gamma_shape = "1.4", prop_invariant = 0.4)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("JC69 JC69 JC69 JC69 shared site model", {
expected <- c(
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_jc69_site_model(id = "anthus_aco"),
create_jc69_site_model(id = "anthus_aco"),
create_jc69_site_model(id = "anthus_aco"),
create_jc69_site_model(id = "anthus_aco")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("HKY 2 HKY 2 HKY 2 HKY 2 GCC diff shapes diff prop_inv", {
expected <- c(
"<parameter id=\"gammaShape.s:anthus_aco\" name=\"stateNode\">1.1</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd2\" name=\"stateNode\">1.2</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd3\" name=\"stateNode\">1.3</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd4\" name=\"stateNode\">1.4</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"kappa.s:anthus_aco\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"kappa.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"kappa.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"kappa.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"freqParameter.s:anthus_nd2\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"freqParameter.s:anthus_nd4\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"freqParameter.s:anthus_nd3\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"freqParameter.s:anthus_aco\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>" # nolint XML is long, so this line is long
)
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_hky_site_model(id = "anthus_aco",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2, gamma_shape = "1.1", prop_invariant = 0.1)
),
create_hky_site_model(id = "anthus_nd2",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2, gamma_shape = "1.2", prop_invariant = 0.2)
),
create_hky_site_model(id = "anthus_nd3",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2, gamma_shape = "1.3", prop_invariant = 0.3)
),
create_hky_site_model(id = "anthus_nd4",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2, gamma_shape = "1.4", prop_invariant = 0.4)
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("aco_nd2_nd3_nd4_complex_2_4.xml state section", {
skip("state, 4 alignments")
expected <- c(
"<parameter id=\"kappa.s:anthus_nd2\" lower=\"0.0\" name=\"stateNode\">2.1</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"kappa1.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">2.2</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"kappa2.s:anthus_nd3\" lower=\"0.0\" name=\"stateNode\">2.3</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"rateAC.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.1</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"rateAG.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.2</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"rateAT.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.3</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"rateCG.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.4</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"rateGT.s:anthus_nd4\" lower=\"0.0\" name=\"stateNode\">1.6</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_aco\" name=\"stateNode\">0.1</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd2\" name=\"stateNode\">0.2</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"gammaShape.s:anthus_nd3\" name=\"stateNode\">0.4</parameter>", # nolint XML is long, so this line is long
"<parameter id=\"freqParameter.s:anthus_nd2\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>" # nolint XML is long, so this line is long
)
# JC69, HKY, TN93, GTR
created <- beautier:::site_models_to_xml_state(
site_models = list(
create_jc69_site_model(
id = "anthus_aco",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 4,
gamma_shape = 0.1,
prop_invariant = 0.7
)
),
create_hky_site_model(
id = "anthus_nd2",
kappa = "2.1",
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 3,
gamma_shape = 0.2,
prop_invariant = 0.6,
freq_equilibrium = "estimated"
)
),
create_tn93_site_model(
id = "anthus_nd3",
kappa_1_param = create_kappa_1_param(value = "2.2"),
kappa_2_param = create_kappa_2_param(value = "2.3"),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 2,
gamma_shape = 0.4,
prop_invariant = 0.6
),
freq_equilibrium = "empirical"
),
create_gtr_site_model(
id = "anthus_nd4",
rate_ac_param = create_rate_ac_param(value = "1.1"),
rate_ag_param = create_rate_ag_param(value = "1.2"),
rate_at_param = create_rate_at_param(value = "1.3"),
rate_cg_param = create_rate_cg_param(value = "1.4"),
rate_ct_param = create_rate_ct_param(value = "1.5"),
rate_gt_param = create_rate_gt_param(value = "1.6"),
gamma_site_model = create_gamma_site_model(
gamma_cat_count = 1,
gamma_shape = 0.8,
prop_invariant = 0.4
),
freq_equilibrium = "all_equal"
)
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.