context("clock_models_to_xml_tracelog")
################################################################################
# Two alignments with unlinked clock models
################################################################################
test_that("RLN RLN ", {
expected <- c(
"<log idref=\"ucldStdev.c:anthus_aco\"/>", # nolint XML
"<log id=\"rate.c:anthus_aco\" spec=\"beast.evolution.branchratemodel.RateStatistic\" branchratemodel=\"@RelaxedClock.c:anthus_aco\" tree=\"@Tree.t:anthus_aco\"/>", # nolint XML
"<log idref=\"ucldMean.c:anthus_nd2\"/>", # nolint XML
"<log idref=\"ucldStdev.c:anthus_nd2\"/>", # nolint XML
"<log id=\"rate.c:anthus_nd2\" spec=\"beast.evolution.branchratemodel.RateStatistic\" branchratemodel=\"@RelaxedClock.c:anthus_nd2\" tree=\"@Tree.t:anthus_nd2\"/>" # nolint XML
)
created <- beautier:::clock_models_to_xml_tracelog(
list(
create_rln_clock_model(id = "anthus_aco"),
create_rln_clock_model(id = "anthus_nd2")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("RLN strict", {
expected <- c(
"<log idref=\"clockRate.c:anthus_nd2\"/>", # nolint XML
"<log idref=\"ucldStdev.c:anthus_aco\"/>", # nolint XML
"<log id=\"rate.c:anthus_aco\" spec=\"beast.evolution.branchratemodel.RateStatistic\" branchratemodel=\"@RelaxedClock.c:anthus_aco\" tree=\"@Tree.t:anthus_aco\"/>" # nolint XML
)
created <- beautier:::clock_models_to_xml_tracelog(
list(
create_rln_clock_model(id = "anthus_aco"),
create_strict_clock_model(id = "anthus_nd2")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("strict RLN", {
expected <- c(
"<log idref=\"ucldMean.c:anthus_nd2\"/>", # nolint XML
"<log idref=\"ucldStdev.c:anthus_nd2\"/>", # nolint XML
"<log id=\"rate.c:anthus_nd2\" spec=\"beast.evolution.branchratemodel.RateStatistic\" branchratemodel=\"@RelaxedClock.c:anthus_nd2\" tree=\"@Tree.t:anthus_nd2\"/>" # nolint XML
)
created <- beautier:::clock_models_to_xml_tracelog(
list(
create_strict_clock_model(id = "anthus_aco"),
create_rln_clock_model(id = "anthus_nd2")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("strict strict", {
expected <- c(
"<log idref=\"clockRate.c:anthus_nd2\"/>" # nolint XML
)
created <- beautier:::clock_models_to_xml_tracelog(
list(
create_strict_clock_model(id = "anthus_aco"),
create_strict_clock_model(id = "anthus_nd2")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
################################################################################
# Two alignments with shared clock models
################################################################################
test_that("shared RLN", {
expected <- c(
"<log idref=\"ucldStdev.c:anthus_aco\"/>", # nolint XML
"<log id=\"rate.c:anthus_aco\" spec=\"beast.evolution.branchratemodel.RateStatistic\" branchratemodel=\"@RelaxedClock.c:anthus_aco\" tree=\"@Tree.t:anthus_aco\"/>" # nolint XML
)
created <- beautier:::clock_models_to_xml_tracelog(
list(
create_rln_clock_model(id = "anthus_aco"),
create_rln_clock_model(id = "anthus_aco")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
test_that("shared strict", {
expected <- c(
# Nothing
)
created <- beautier:::clock_models_to_xml_tracelog(
list(
create_strict_clock_model(id = "anthus_aco"),
create_strict_clock_model(id = "anthus_aco")
)
)
testthat::expect_true(beautier:::are_equivalent_xml_lines(created, expected))
})
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