Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----check_empty_cache_at_start, include = FALSE------------------------------
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
## ----load_babette, results='hide', warning=FALSE, error=FALSE, message=FALSE----
library(babette)
## -----------------------------------------------------------------------------
posterior <- create_test_bbt_run_output()
posterior$anthus_aco_sub_trees <- posterior$anthus_aco_trees
names(posterior)
## -----------------------------------------------------------------------------
fasta_filename <- get_babette_path("anthus_aco_sub.fas")
## -----------------------------------------------------------------------------
mcmc <- create_test_mcmc(chain_length = 10000)
## ----example_1, cache=TRUE----------------------------------------------------
if (is_beast2_installed()) {
inference_model <- create_inference_model(
mcmc = mcmc
)
beast2_options <- create_beast2_options()
posterior <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## ----fig.width=7, fig.height=7------------------------------------------------
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)
## -----------------------------------------------------------------------------
mcmc <- create_test_mcmc(chain_length = 10000)
## ----example_2_mrca, cache=FALSE----------------------------------------------
if (is_beast2_installed()) {
inference_model <- create_inference_model(
mcmc = mcmc,
mrca_prior = create_mrca_prior(
taxa_names = sample(get_taxa_names(fasta_filename), size = 3),
alignment_id = get_alignment_id(fasta_filename),
is_monophyletic = TRUE,
mrca_distr = create_normal_distr(
mean = 15.0,
sigma = 0.025
)
)
)
beast2_options <- create_beast2_options()
posterior <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## ----fig.width=7, fig.height=7------------------------------------------------
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)
## ----example_3, cache=TRUE----------------------------------------------------
if (is_beast2_installed()) {
inference_model <- create_inference_model(
site_model = create_jc69_site_model(),
mcmc = mcmc
)
beast2_options <- create_beast2_options()
posterior <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## ----fig.width=7, fig.height=7------------------------------------------------
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)
## ----example_4, cache=TRUE----------------------------------------------------
if (is_beast2_installed()) {
inference_model <- create_inference_model(
clock_model = create_rln_clock_model(),
mcmc = mcmc
)
beast2_options <- create_beast2_options()
posterior <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## ----fig.width=7, fig.height=7------------------------------------------------
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)
## ----example_5, cache=TRUE----------------------------------------------------
if (is_beast2_installed()) {
inference_model <- create_inference_model(
tree_prior = create_bd_tree_prior(),
mcmc = mcmc
)
beast2_options <- create_beast2_options()
posterior <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## ----fig.width=7, fig.height=7------------------------------------------------
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)
## ----example_6, cache=TRUE----------------------------------------------------
if (is_beast2_installed()) {
inference_model <- create_inference_model(
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_normal_distr(
mean = 1.0,
sigma = 0.1
)
),
mcmc = mcmc
)
beast2_options <- create_beast2_options()
posterior <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## ----fig.width=7, fig.height=7------------------------------------------------
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)
## ----example_7, cache=TRUE----------------------------------------------------
if (is_beast2_installed()) {
inference_model <- create_inference_model(
site_model = create_hky_site_model(
gamma_site_model = create_gamma_site_model(prop_invariant = 0.5)
),
mcmc = mcmc
)
beast2_options <- create_beast2_options()
posterior <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## ----fig.width=7, fig.height=7------------------------------------------------
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)
## ----example_8, cache=TRUE----------------------------------------------------
if (is_beast2_installed()) {
inference_model <- create_inference_model(
clock_model = create_strict_clock_model(
clock_rate_param = 0.5
),
mcmc = mcmc
)
beast2_options <- create_beast2_options()
posterior <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## ----fig.width=7, fig.height=7------------------------------------------------
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)
## ----check_empty_cache_at_end, include = FALSE--------------------------------
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
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