context("tree_priors_to_xml_state")
test_that("Yule Yule Yule Yule", {
expected <- c(
"<parameter id=\"birthRate.t:anthus_aco\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"birthRate.t:anthus_nd2\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"birthRate.t:anthus_nd3\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"birthRate.t:anthus_nd4\" name=\"stateNode\">1.0</parameter>" # nolint XML can be long
)
created <- beautier:::tree_priors_to_xml_state(
tree_priors = list(
create_yule_tree_prior(id = "anthus_aco"),
create_yule_tree_prior(id = "anthus_nd2"),
create_yule_tree_prior(id = "anthus_nd3"),
create_yule_tree_prior(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("BD BD BD BD", {
expected <- c(
"<parameter id=\"BDBirthRate.t:anthus_aco\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_aco\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>", # nolint XML can be long
"<parameter id=\"BDBirthRate.t:anthus_nd2\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_nd2\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>", # nolint XML can be long
"<parameter id=\"BDBirthRate.t:anthus_nd3\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_nd3\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>", # nolint XML can be long
"<parameter id=\"BDBirthRate.t:anthus_nd4\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_nd4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>" # nolint XML can be long
)
created <- beautier:::tree_priors_to_xml_state(
tree_priors = list(
create_bd_tree_prior(id = "anthus_aco"),
create_bd_tree_prior(id = "anthus_nd2"),
create_bd_tree_prior(id = "anthus_nd3"),
create_bd_tree_prior(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("CBS CBS CBS CBS", {
expected <- c(
"<parameter id=\"bPopSizes.t:anthus_aco\" dimension=\"5\" lower=\"0.0\" name=\"stateNode\" upper=\"380000.0\">380.0</parameter>", # nolint XML can be long
"<stateNode id=\"bGroupSizes.t:anthus_aco\" spec=\"parameter.IntegerParameter\" dimension=\"5\">1</stateNode>", # nolint XML can be long
"<parameter id=\"bPopSizes.t:anthus_nd4\" dimension=\"5\" lower=\"0.0\" name=\"stateNode\" upper=\"380000.0\">380.0</parameter>", # nolint XML can be long
"<stateNode id=\"bGroupSizes.t:anthus_nd4\" spec=\"parameter.IntegerParameter\" dimension=\"5\">1</stateNode>", # nolint XML can be long
"<parameter id=\"bPopSizes.t:anthus_nd2\" dimension=\"5\" lower=\"0.0\" name=\"stateNode\" upper=\"380000.0\">380.0</parameter>", # nolint XML can be long
"<stateNode id=\"bGroupSizes.t:anthus_nd2\" spec=\"parameter.IntegerParameter\" dimension=\"5\">1</stateNode>", # nolint XML can be long
"<parameter id=\"bPopSizes.t:anthus_nd3\" dimension=\"5\" lower=\"0.0\" name=\"stateNode\" upper=\"380000.0\">380.0</parameter>", # nolint XML can be long
"<stateNode id=\"bGroupSizes.t:anthus_nd3\" spec=\"parameter.IntegerParameter\" dimension=\"5\">1</stateNode>" # nolint XML can be long
)
created <- beautier:::tree_priors_to_xml_state(
tree_priors = list(
create_cbs_tree_prior(id = "anthus_aco"),
create_cbs_tree_prior(id = "anthus_nd2"),
create_cbs_tree_prior(id = "anthus_nd3"),
create_cbs_tree_prior(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("CCP CCP CCP CCP", {
expected <- c(
"<parameter id=\"popSize.t:anthus_nd2\" name=\"stateNode\">0.3</parameter>",
"<parameter id=\"popSize.t:anthus_nd3\" name=\"stateNode\">0.3</parameter>",
"<parameter id=\"popSize.t:anthus_nd4\" name=\"stateNode\">0.3</parameter>",
"<parameter id=\"popSize.t:anthus_aco\" name=\"stateNode\">0.3</parameter>"
)
created <- beautier:::tree_priors_to_xml_state(
tree_priors = list(
create_ccp_tree_prior(id = "anthus_aco"),
create_ccp_tree_prior(id = "anthus_nd2"),
create_ccp_tree_prior(id = "anthus_nd3"),
create_ccp_tree_prior(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("CEP CEP CEP CEP", {
expected <- c(
"<parameter id=\"ePopSize.t:anthus_aco\" name=\"stateNode\">0.3</parameter>", # nolint XML can be long
"<parameter id=\"growthRate.t:anthus_aco\" name=\"stateNode\">3.0E-4</parameter>", # nolint XML can be long
"<parameter id=\"ePopSize.t:anthus_nd4\" name=\"stateNode\">0.3</parameter>", # nolint XML can be long
"<parameter id=\"growthRate.t:anthus_nd4\" name=\"stateNode\">3.0E-4</parameter>", # nolint XML can be long
"<parameter id=\"ePopSize.t:anthus_nd3\" name=\"stateNode\">0.3</parameter>", # nolint XML can be long
"<parameter id=\"growthRate.t:anthus_nd3\" name=\"stateNode\">3.0E-4</parameter>", # nolint XML can be long
"<parameter id=\"ePopSize.t:anthus_nd2\" name=\"stateNode\">0.3</parameter>", # nolint XML can be long
"<parameter id=\"growthRate.t:anthus_nd2\" name=\"stateNode\">3.0E-4</parameter>" # nolint XML can be long
)
created <- beautier:::tree_priors_to_xml_state(
tree_priors = list(
create_cep_tree_prior(id = "anthus_aco"),
create_cep_tree_prior(id = "anthus_nd2"),
create_cep_tree_prior(id = "anthus_nd3"),
create_cep_tree_prior(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("Yule Yule Yule BD", {
expected <- c(
"<parameter id=\"birthRate.t:anthus_aco\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"birthRate.t:anthus_nd2\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"birthRate.t:anthus_nd3\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDBirthRate.t:anthus_nd4\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_nd4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>" # nolint XML can be long
)
created <- beautier:::tree_priors_to_xml_state(
tree_priors = list(
create_yule_tree_prior(id = "anthus_aco"),
create_yule_tree_prior(id = "anthus_nd2"),
create_yule_tree_prior(id = "anthus_nd3"),
create_bd_tree_prior(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("Yule Yule BD BD", {
expected <- c(
"<parameter id=\"birthRate.t:anthus_aco\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"birthRate.t:anthus_nd2\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDBirthRate.t:anthus_nd4\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_nd4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>", # nolint XML can be long
"<parameter id=\"BDBirthRate.t:anthus_nd3\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_nd3\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>" # nolint XML can be long
)
created <- beautier:::tree_priors_to_xml_state(
tree_priors = list(
create_yule_tree_prior(id = "anthus_aco"),
create_yule_tree_prior(id = "anthus_nd2"),
create_bd_tree_prior(id = "anthus_nd3"),
create_bd_tree_prior(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("BD Yule Yule BD", {
expected <- c(
"<parameter id=\"BDBirthRate.t:anthus_aco\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_aco\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>", # nolint XML can be long
"<parameter id=\"birthRate.t:anthus_nd2\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"birthRate.t:anthus_nd3\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDBirthRate.t:anthus_nd4\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_nd4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>" # nolint XML can be long
)
created <- beautier:::tree_priors_to_xml_state(
tree_priors = list(
create_bd_tree_prior(id = "anthus_aco"),
create_yule_tree_prior(id = "anthus_nd2"),
create_yule_tree_prior(id = "anthus_nd3"),
create_bd_tree_prior(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("BD BD Yule Yule", {
expected <- c(
"<parameter id=\"birthRate.t:anthus_nd3\" name=\"stateNode\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDBirthRate.t:anthus_aco\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_aco\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>", # nolint XML can be long
"<parameter id=\"BDBirthRate.t:anthus_nd2\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>", # nolint XML can be long
"<parameter id=\"BDDeathRate.t:anthus_nd2\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>", # nolint XML can be long
"<parameter id=\"birthRate.t:anthus_nd4\" name=\"stateNode\">1.0</parameter>" # nolint XML can be long
)
created <- beautier:::tree_priors_to_xml_state(
tree_priors = list(
create_bd_tree_prior(id = "anthus_aco"),
create_bd_tree_prior(id = "anthus_nd2"),
create_yule_tree_prior(id = "anthus_nd3"),
create_yule_tree_prior(id = "anthus_nd4")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
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