pir_to_pics | R Documentation |
These are the files created:
true_tree.png
the true/given phylogeny
true_alignment.png
the alignment simulated from the
true/given phylogeny
twin_tree.png
the twin tree [1]
twin_alignment.png
the alignment simulated from the
twin phylogeny
true_posterior_gen.png
the phylogenies of the Bayesian posterior,
using a generative inference model,
based on the alignment based on the true tree
twin_posterior_gen.png
the phylogenies of the Bayesian posterior,
using a generative inference model,
based on the alignment based on the twin tree
true_error_histogram_gen.png
the errors between the Bayesian posterior
and true/given tree,
using a generative inference model,
plotted as a histogram
twin_error_histogram_gen.png
the errors between the Bayesian posterior
and twin tree,
using a generative inference model,
plotted as a histogram
true_error_violin_gen.png
the errors between the Bayesian posterior
and true/given tree,
using a generative inference model,
plotted as a violin plot
twin_error_violin_gen.png
the errors between the Bayesian posterior
and twin tree,
using a generative inference model,
plotted as a violin plot
true_posterior_best.png
the phylogenies of the Bayesian posterior,
using the best candidate inference model,
based on the alignment based on the true tree
twin_posterior_best.png
the phylogenies of the Bayesian posterior,
using the best candidate inference model,
based on the alignment based on the twin tree
true_error_histogram_best.png
the errors between the Bayesian posterior
and true/given tree,
using the best candidate inference model,
plotted as a histogram
twin_error_histogram_best.png
the errors between the Bayesian posterior
and twin tree,
using the best candidate inference model,
plotted as a histogram
true_error_violin_best.png
the errors between the Bayesian posterior
and true/given tree,
using the best candidate inference model,
plotted as a violin plot
twin_error_violin_best.png
the errors between the Bayesian posterior
and twin tree,
using the best candidate inference model,
plotted as a violin plot
Items marked [1] are created dependent on the setup.
pir_to_pics(
phylogeny,
pir_params,
consensus = rev(sort(phylogeny$tip.label)),
folder = tempdir()
)
phylogeny |
a phylogeny of class phylo |
pir_params |
the parameters of pirouette. They are created by create_pir_params. |
consensus |
the order of which the taxon labels are plotted |
folder |
folder where the files are stored in. By default, this is a temporary folder |
the names of all files created
Richèl J.C. Bilderbeek
if (beautier::is_on_ci()) {
phylogeny <- ape::read.tree(text = "((A:1, B:1):1, C:2);")
pir_params <- create_test_pir_params(
twinning_params = create_twinning_params()
)
if (rappdirs::app_dir()$os != "win" &&
beautier::is_on_ci() && beastier::is_beast2_installed()
) {
pir_out <- pir_run(phylogeny = phylogeny, pir_params = pir_params)
folder <- tempdir()
expected_filenames <- c(
file.path(folder, "true_tree.png"),
file.path(folder, "true_alignment.png"),
file.path(folder, "twin_tree.png"),
file.path(folder, "twin_alignment.png"),
file.path(folder, "true_posterior_gen.png"),
file.path(folder, "twin_posterior_gen.png"),
file.path(folder, "true_error_histogram_gen.png"),
file.path(folder, "twin_error_histogram_gen.png"),
file.path(folder, "true_error_violin_gen.png"),
file.path(folder, "twin_error_violin_gen.png")
)
# created_filenames are the filenames of the pictures
created_filenames <- pir_to_pics(
phylogeny = phylogeny,
pir_params = pir_params,
folder = folder
)
}
}
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