View source: R/create_pir_params.R
create_test_pir_params | R Documentation |
Create a set of testing parameters for pirouette
create_test_pir_params(
alignment_params = create_test_alignment_params(),
twinning_params = NA,
experiments = list(create_test_experiment()),
error_measure_params = create_error_measure_params(),
evidence_filename = NA,
verbose = FALSE
)
alignment_params |
parameters to simulate an alignment, as can be created by create_alignment_params |
twinning_params |
can be |
experiments |
a list of one or more pirouette experiments, as can be created by create_experiment. If more than one experiment is provided and a "generative" experiment is part of them, the "generative" one has to be the first in the list. See also:
|
error_measure_params |
parameter set to specify how the error between the given phylogeny and the Bayesian posterior is determined. Use create_error_measure_params to create such a parameter set |
evidence_filename |
filename to store the estimated evidences (aka marginal likelihoods), as can be created by get_temp_evidence_filename. Must be NA if there is evidence estimation (as determined by will_measure_evidence). |
verbose |
if TRUE, show more output |
a list with all pirouette parameters
Richèl J.C. Bilderbeek
Use create_test_pir_params_setup to create
a test pir_params
following a specific setup, such as
having a candidate experiemnt and/or use twinning.
if (rappdirs::app_dir()$os != "win" &&
beautier::is_on_ci() &&
beastier::is_beast2_installed()
) {
pir_params <- create_test_pir_params()
check_pir_params(pir_params)
pir_out <- pir_run(
phylogeny = ape::read.tree(text = "((A:1, B:1):1, C:2);"),
pir_params = pir_params
)
pir_plot(pir_out)
}
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