View source: R/create_twinning_params.R
create_twinning_params | R Documentation |
The site model and clock models will be used and their combination will be called the generative model of the twinning.
create_twinning_params(
rng_seed_twin_tree = 0,
sim_twin_tree_fun = get_sim_bd_twin_tree_fun(),
rng_seed_twin_alignment = 0,
sim_twal_fun = get_sim_twal_with_std_nsm_fun(),
twin_tree_filename = to_twin_filename(get_temp_tree_filename()),
twin_alignment_filename = to_twin_filename(get_temp_fasta_filename()),
twin_evidence_filename = NA
)
rng_seed_twin_tree |
the random number generator seed as used in the simulation of a twin tree |
sim_twin_tree_fun |
function to simulate a twin tree with.
This function must have one argument called Some standard functions:
|
rng_seed_twin_alignment |
the random number generator seed as used in the simulation of a twin alignment |
sim_twal_fun |
function to simulate a
twin alignment with.
This function must have two arguments called Use check_sim_twal_fun to verify if the function has the right signature and output. Some standard functions:
|
twin_tree_filename |
name of the ( |
twin_alignment_filename |
name of the FASTA file the twin alignment will be saved to |
twin_evidence_filename |
filename to store the estimated evidences (aka marginal likelihoods) of the twin tree |
a twinning parameter set
Richèl J.C. Bilderbeek, Giovanni Laudanno
if (beautier::is_on_ci()) {
twinning_params <- create_twinning_params()
check_twinning_params(twinning_params)
pir_params <- create_test_pir_params(
twinning_params = twinning_params
)
check_pir_params(pir_params)
if (beautier::is_on_ci() &&
rappdirs::app_dir()$os == "unix" &&
beastier::is_beast2_installed()) {
pir_out <- pir_run(
phylogeny = ape::read.tree(text = "((A:1, B:1):1, C:2);"),
pir_params = pir_params
)
}
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.