View source: R/create_pir_params.R
create_pir_params | R Documentation |
Create the parameters for pirouette
create_pir_params(
alignment_params,
twinning_params = NA,
experiments = list(create_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
Giovanni Laudanno, Richèl J.C. Bilderbeek
Use pir_run to run the pirouette pipeline
Use create_test_pir_params to create
a test pir_params
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 (beautier::is_on_ci()) {
# Create all elements to create a pirouette parameter set
alignment_params <- create_test_alignment_params()
twinning_params <- create_twinning_params()
experiments <- list(create_test_gen_experiment())
error_measure_params <- create_error_measure_params()
evidence_filename <- NA
verbose <- FALSE
# Create the pirouette parameter set
pir_params <- create_pir_params(
alignment_params = alignment_params,
twinning_params = twinning_params,
experiments = experiments,
error_measure_params = error_measure_params,
evidence_filename = evidence_filename,
verbose = verbose
)
# Run that experiment on a continuous integration service,
# only when BEAST2 is unstalled
if (rappdirs::app_dir()$os != "win" &&
beautier::is_on_ci() && beastier::is_beast2_installed()
) {
pir_out <- pir_run(
phylogeny = ape::read.tree(text = "((A:2, B:2):1, C:3);"),
pir_params = pir_params
)
pir_plot(pir_out)
}
}
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