knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
file.copy(babette::get_babette_path("anthus_aco_sub.fas"), "test_output_0.fas") file.copy(babette::get_babette_path("anthus_aco_sub.fas"), "my_fasta.fas") file.copy(babette::get_babette_path("anthus_aco_sub.fas"), "my_alignment.fas") file.copy(babette::get_babette_path("anthus_aco_sub.fas"), "anthus_aco.fas") file.copy(babette::get_babette_path("anthus_nd2_sub.fas"), "anthus_nd2.fas")
This vignette does the same as the code in the bioRxiv article.
library(babette) mcmc <- create_mcmc(chain_length = 2000, store_every = 1000)
out <- bbt_run( fasta_filenames = "anthus_aco.fas", mcmc = mcmc )
out <- bbt_run( "anthus_aco.fas", site_models = create_hky_site_model(), clock_models = create_rln_clock_model(), tree_priors = create_bd_tree_prior(), mcmc = mcmc )
# Currently, support for multiple alignments has been deprecated if (1 == 2) { out <- bbt_run( c("anthus_aco.fas", "anthus_nd2.fas"), site_models = list( create_tn93_site_model(), create_gtr_site_model() ), mcmc = mcmc ) }
out <- bbt_run( "anthus_aco.fas", tree_priors = create_yule_tree_prior( birth_rate_distr = create_exp_distr() ), mcmc = mcmc )
out <- bbt_run( "anthus_aco.fas", tree_priors = create_yule_tree_prior( birth_rate_distr = create_exp_distr( mean = 1.0 ) ), mcmc = mcmc )
out <- bbt_run( "anthus_aco.fas", posterior_crown_age = 15, mcmc = mcmc )
out <- bbt_run( "anthus_aco.fas", mrca_priors = create_mrca_prior( alignment_id = get_alignment_id("anthus_aco.fas"), taxa_names = get_taxa_names("anthus_aco.fas"), mrca_distr = create_normal_distr( mean = 15.0, sigma = 0.01 ) ), mcmc = mcmc )
traces <- remove_burn_ins( traces = out$estimates, burn_in_fraction = 0.2 )
esses <- calc_esses( traces = traces, sample_interval = 1000 )
sum_stats <- calc_summary_stats( traces = traces, sample_interval = 1000 )
plot_densitree(phylos = out$anthus_aco_trees)
file.remove("test_output_0.fas") file.remove("my_fasta.fas") file.remove("my_alignment.fas") file.remove("anthus_aco.fas") file.remove("anthus_nd2.fas")
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