Title: | Control 'BEAST2' |
---|---|
Description: | 'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'. |
Authors: | Richèl J.C. Bilderbeek [aut, cre] , Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci, see https://github.com/richelbilderbeek/onboarding/issues/209), David Winter [rev] (David reviewed the package for rOpenSci, see https://github.com/richelbilderbeek/onboarding/issues/209), Jason Griffiths [ctb] , Olivier Roy [ctb], Giovanni Laudanno [ctb] |
Maintainer: | Richèl J.C. Bilderbeek <[email protected]> |
License: | GPL-3 |
Version: | 2.3.4 |
Built: | 2024-09-25 05:47:47 UTC |
Source: | https://github.com/ropensci/babette |
Do a full run: create a 'BEAST2' configuration file (like 'BEAUti 2'), run 'BEAST2', parse results (like 'Tracer')
bbt_continue(fasta_filename, inference_model, beast2_options)
bbt_continue(fasta_filename, inference_model, beast2_options)
fasta_filename |
a FASTA filename |
inference_model |
a Bayesian phylogenetic inference model, as returned by create_inference_model |
beast2_options |
'BEAST2' options, as can be created by create_beast2_options |
a list with the following elements:
estimates
: a data frame with 'BEAST2'
parameter estimates
[alignment_id]_trees
: a multiPhylo
containing the phylogenies
in the 'BEAST2' posterior. [alignment_id]
is the ID of the alignment. For example,
when running bbt_run_from_model
with
anthus_aco.fas
, this element will have
name anthus_aco_trees
operators
: a data frame with the
'BEAST2' MCMC operator acceptances
output
: a numeric vector with the output
sent to standard output and error streams
ns
: (optional) the results of a marginal likelihood estimation,
will exist only when create_ns_mcmc
was
used for mcmc
.
This structure will contain the following elements:
marg_log_lik
the marginal log likelihood estimate
marg_log_lik_sd
the standard deviation around the estimate
estimates
the parameter estimates
created during the marginal likelihood estimation
trees
the trees
created during the marginal likelihood estimation
Richèl J.C. Bilderbeek
Use remove_burn_ins
to remove the burn-ins from
the posterior's estimates (posterior$estimates
)
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # A simple FASTA file fasta_filename <- beautier::get_beautier_path("test_output_0.fas") # Simple short inference inference_model <- create_test_inference_model() # Default BEAST2 options beast2_options <- create_beast2_options() bbt_run_from_model( fasta_filename = fasta_filename, inference_model = inference_model, beast2_options = beast2_options ) bbt_continue( fasta_filename = fasta_filename, inference_model = inference_model, beast2_options = beast2_options ) # Cleanup bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # A simple FASTA file fasta_filename <- beautier::get_beautier_path("test_output_0.fas") # Simple short inference inference_model <- create_test_inference_model() # Default BEAST2 options beast2_options <- create_beast2_options() bbt_run_from_model( fasta_filename = fasta_filename, inference_model = inference_model, beast2_options = beast2_options ) bbt_continue( fasta_filename = fasta_filename, inference_model = inference_model, beast2_options = beast2_options ) # Cleanup bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
Delete all the temporary files created by bbt_run_from_model
bbt_delete_temp_files(inference_model, beast2_options)
bbt_delete_temp_files(inference_model, beast2_options)
inference_model |
a Bayesian phylogenetic inference model, as returned by create_inference_model |
beast2_options |
'BEAST2' options, as can be created by create_beast2_options |
Nothing.
Richèl J.C. Bilderbeek
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # Do a minimal run inference_model <- create_test_inference_model() beast2_options <- create_beast2_options() bbt_run_from_model( fasta_filename = get_fasta_filename(), inference_model = inference_model, beast2_options = beast2_options ) # Cleanup bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # Do a minimal run inference_model <- create_test_inference_model() beast2_options <- create_beast2_options() bbt_run_from_model( fasta_filename = get_fasta_filename(), inference_model = inference_model, beast2_options = beast2_options ) # Cleanup bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
Do a full BEAST2 run: create a 'BEAST2' configuration file (like 'BEAUti 2'), run 'BEAST2', parse results (like 'Tracer')
bbt_run( fasta_filename, tipdates_filename = NA, site_model = beautier::create_jc69_site_model(), clock_model = beautier::create_strict_clock_model(), tree_prior = beautier::create_yule_tree_prior(), mrca_prior = NA, mcmc = beautier::create_mcmc(), beast2_input_filename = beastier::create_temp_input_filename(), rng_seed = 1, beast2_output_state_filename = beastier::create_temp_state_filename(), beast2_path = beastier::get_default_beast2_path(), overwrite = TRUE, verbose = FALSE )
bbt_run( fasta_filename, tipdates_filename = NA, site_model = beautier::create_jc69_site_model(), clock_model = beautier::create_strict_clock_model(), tree_prior = beautier::create_yule_tree_prior(), mrca_prior = NA, mcmc = beautier::create_mcmc(), beast2_input_filename = beastier::create_temp_input_filename(), rng_seed = 1, beast2_output_state_filename = beastier::create_temp_state_filename(), beast2_path = beastier::get_default_beast2_path(), overwrite = TRUE, verbose = FALSE )
fasta_filename |
a FASTA filename |
tipdates_filename |
name of the file containing tip dates |
site_model |
one site model, see create_site_models |
clock_model |
one clock model, see create_clock_model |
tree_prior |
one tree priors, as created by create_tree_prior |
mrca_prior |
one Most Recent Common Ancestor prior,
as returned by |
mcmc |
the MCMC options, see create_mcmc |
beast2_input_filename |
path of the 'BEAST2' configuration file.
By default, this file is put in a temporary folder with a random
filename, as the user needs not read it: it is used as input of 'BEAST2'.
Specifying a |
rng_seed |
the random number generator seed. Must be either
|
beast2_output_state_filename |
name of the final state file created
by 'BEAST2', containing the operator acceptances. By default, this
file is put a temporary folder with a random
filename, as the user needs not read it: its content
is parsed and returned by this function.
Specifying a |
beast2_path |
name of either a 'BEAST2' binary file
(usually simply |
overwrite |
will 'BEAST2' overwrite files? Like 'BEAST2',
this is set to TRUE by default.
If TRUE, 'BEAST2' will overwrite the
|
verbose |
set to TRUE for more output |
Prefer using bbt_run_from_model
, as it has a cleaner interface.
a list with the following elements:
estimates
: a data frame with 'BEAST2'
parameter estimates
[alignment_id]_trees
: a multiPhylo
containing the phylogenies
in the 'BEAST2' posterior. [alignment_id]
is the ID of the alignment. For example,
when running bbt_run
with
anthus_aco.fas
, this element will have
name anthus_aco_trees
operators
: a data frame with the
'BEAST2' MCMC operator acceptances
output
: a numeric vector with the output
sent to standard output and error streams
ns
: (optional) the results of a marginal likelihood estimation,
will exist only when create_ns_mcmc
was
used for the MCMC.
This structure will contain the following elements:
marg_log_lik
the marginal log likelihood estimate
marg_log_lik_sd
the standard deviation around the estimate
estimates
the parameter estimates
created during the marginal likelihood estimation
trees
the trees
created during the marginal likelihood estimation
Richèl J.C. Bilderbeek
Use remove_burn_ins
to remove the burn-ins from
the posterior's estimates (posterior$estimates
)
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # Setup for a short run mcmc <- create_test_mcmc() # Store filenames for cleanup. # Note that 'bbt_run_from_model allows for easier cleanup mcmc$tracelog$filename <- tempfile() mcmc$treelog$filename <- tempfile() mcmc$screenlog$filename <- tempfile() beast2_input_filename <- tempfile() beast2_output_state_filename <- tempfile() bbt_run( fasta_filename = get_babette_path("anthus_aco.fas"), beast2_input_filename = beast2_input_filename, beast2_output_state_filename = beast2_output_state_filename, mcmc = mcmc ) # Cleanup # Again, note that 'bbt_run_from_model allows for easier cleanup file.remove(mcmc$tracelog$filename) file.remove(mcmc$treelog$filename) file.remove(mcmc$screenlog$filename) file.remove(beast2_input_filename) file.remove(beast2_output_state_filename) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # Setup for a short run mcmc <- create_test_mcmc() # Store filenames for cleanup. # Note that 'bbt_run_from_model allows for easier cleanup mcmc$tracelog$filename <- tempfile() mcmc$treelog$filename <- tempfile() mcmc$screenlog$filename <- tempfile() beast2_input_filename <- tempfile() beast2_output_state_filename <- tempfile() bbt_run( fasta_filename = get_babette_path("anthus_aco.fas"), beast2_input_filename = beast2_input_filename, beast2_output_state_filename = beast2_output_state_filename, mcmc = mcmc ) # Cleanup # Again, note that 'bbt_run_from_model allows for easier cleanup file.remove(mcmc$tracelog$filename) file.remove(mcmc$treelog$filename) file.remove(mcmc$screenlog$filename) file.remove(beast2_input_filename) file.remove(beast2_output_state_filename) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
Do a full run: create a 'BEAST2' configuration file (like 'BEAUti 2'), run 'BEAST2', parse results (like 'Tracer')
bbt_run_from_model( fasta_filename, inference_model = beautier::create_inference_model(), beast2_options = beastier::create_beast2_options() )
bbt_run_from_model( fasta_filename, inference_model = beautier::create_inference_model(), beast2_options = beastier::create_beast2_options() )
fasta_filename |
a FASTA filename |
inference_model |
a Bayesian phylogenetic inference model, as returned by create_inference_model |
beast2_options |
'BEAST2' options, as can be created by create_beast2_options |
a list with the following elements:
estimates
: a data frame with 'BEAST2'
parameter estimates
[alignment_id]_trees
: a multiPhylo
containing the phylogenies
in the 'BEAST2' posterior. [alignment_id]
is the ID of the alignment. For example,
when running bbt_run_from_model
with
anthus_aco.fas
, this element will have
name anthus_aco_trees
operators
: a data frame with the
'BEAST2' MCMC operator acceptances
output
: a numeric vector with the output
sent to standard output and error streams
ns
: (optional) the results of a marginal likelihood estimation,
will exist only when create_ns_mcmc
was
used for mcmc
.
This structure will contain the following elements:
marg_log_lik
the marginal log likelihood estimate
marg_log_lik_sd
the standard deviation around the estimate
estimates
the parameter estimates
created during the marginal likelihood estimation
trees
the trees
created during the marginal likelihood estimation
Richèl J.C. Bilderbeek
Use remove_burn_ins
to remove the burn-ins from
the posterior's estimates (posterior$estimates
)
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # Simple short inference inference_model <- create_test_inference_model() # Default BEAST2 options beast2_options <- create_beast2_options() bbt_run_from_model( fasta_filename = get_babette_path("anthus_aco.fas"), inference_model = inference_model, beast2_options = beast2_options ) # Cleanup bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # Simple short inference inference_model <- create_test_inference_model() # Default BEAST2 options beast2_options <- create_beast2_options() bbt_run_from_model( fasta_filename = get_babette_path("anthus_aco.fas"), inference_model = inference_model, beast2_options = beast2_options ) # Cleanup bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
Do a self test to verify babette that works correctly.
bbt_self_test(beast2_options = beastier::create_beast2_options())
bbt_self_test(beast2_options = beastier::create_beast2_options())
beast2_options |
'BEAST2' options, as can be created by create_beast2_options |
Nothing. Will raise an exception if something is wrong.
Richèl J.C. Bilderbeek
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() bbt_self_test() beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() bbt_self_test() beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
bbt_run
has the 'BEAST2' packages needed to process
its arguments. Will stop if not.For example, to use a Nested Sampling MCMC, the 'BEAST2' 'NS' package needs to be installed.
check_beast2_pkgs(mcmc, beast2_path = get_default_beast2_bin_path())
check_beast2_pkgs(mcmc, beast2_path = get_default_beast2_bin_path())
mcmc |
the MCMC options, see create_mcmc |
beast2_path |
name of either a 'BEAST2' binary file
(usually simply |
Nothing.
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # Minimal BEAST2 setup check_beast2_pkgs(mcmc = create_mcmc()) # BEAST2 with NS package installed if (is_beast2_ns_pkg_installed()) { check_beast2_pkgs(mcmc = create_ns_mcmc()) } beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # Minimal BEAST2 setup check_beast2_pkgs(mcmc = create_mcmc()) # BEAST2 with NS package installed if (is_beast2_ns_pkg_installed()) { check_beast2_pkgs(mcmc = create_ns_mcmc()) } beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
bbt_run
or bbt_run_from_model
.This output is used in testing.
create_test_bbt_run_output()
create_test_bbt_run_output()
the same results as bbt_run
or bbt_run_from_model
Richèl J.C. Bilderbeek
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() create_test_bbt_run_output() beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() create_test_bbt_run_output() beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
Create testing output similar to when running a 'BEAST2' run with nested sampling
create_test_ns_output()
create_test_ns_output()
a text of type character vector.
Richèl J.C. Bilderbeek
Use parse_beast2_output_to_ns to parse this output to a Nested Sampling result. See create_ns_mcmc to see how to do a marginal likelihood estimation using Nested Sampling.
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() create_test_ns_output() beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() create_test_ns_output() beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
This function does nothing. It is intended to inherit is parameters' documentation.
default_params_doc( beast2_input_filename, beast2_options, beast2_output_log_filename, beast2_output_state_filename, beast2_output_trees_filenames, beast2_path, beast2_working_dir, cleanup, clock_model, clock_models, fasta_filename, fasta_filenames, inference_model, mcmc, mrca_prior, mrca_priors, overwrite, rng_seed, site_model, site_models, tipdates_filename, tree_prior, tree_priors, verbose )
default_params_doc( beast2_input_filename, beast2_options, beast2_output_log_filename, beast2_output_state_filename, beast2_output_trees_filenames, beast2_path, beast2_working_dir, cleanup, clock_model, clock_models, fasta_filename, fasta_filenames, inference_model, mcmc, mrca_prior, mrca_priors, overwrite, rng_seed, site_model, site_models, tipdates_filename, tree_prior, tree_priors, verbose )
beast2_input_filename |
path of the 'BEAST2' configuration file.
By default, this file is put in a temporary folder with a random
filename, as the user needs not read it: it is used as input of 'BEAST2'.
Specifying a |
beast2_options |
'BEAST2' options, as can be created by create_beast2_options |
beast2_output_log_filename |
name of the log file created by 'BEAST2',
containing the parameter estimates in time. By default, this
file is put a temporary folder with a random
filename, as the user needs not read it: its content
is parsed and returned by this function.
Specifying a |
beast2_output_state_filename |
name of the final state file created
by 'BEAST2', containing the operator acceptances. By default, this
file is put a temporary folder with a random
filename, as the user needs not read it: its content
is parsed and returned by this function.
Specifying a |
beast2_output_trees_filenames |
name of the one or more trees
files created by 'BEAST2', one per alignment. By default, these
files are put a temporary folder with a random
filename, as the user needs not read it: their content
is parsed and returned by this function.
Specifying |
beast2_path |
name of either a 'BEAST2' binary file
(usually simply |
beast2_working_dir |
the folder 'BEAST2' will work in. This is an (empty) temporary folder by default. This allows to call 'BEAST2' in multiple parallel processes, as each process can have its own working directory |
cleanup |
set to FALSE to keep all temporary files |
clock_model |
one clock model, see create_clock_model |
clock_models |
one or more clock models, see create_clock_models |
fasta_filename |
a FASTA filename |
fasta_filenames |
one or more FASTA filename, each with one alignment |
inference_model |
a Bayesian phylogenetic inference model, as returned by create_inference_model |
mcmc |
the MCMC options, see create_mcmc |
mrca_prior |
one Most Recent Common Ancestor prior,
as returned by |
mrca_priors |
a list of one or more Most Recent Common Ancestor priors,
as returned by |
overwrite |
will 'BEAST2' overwrite files? Like 'BEAST2',
this is set to TRUE by default.
If TRUE, 'BEAST2' will overwrite the
|
rng_seed |
the random number generator seed. Must be either
|
site_model |
one site model, see create_site_models |
site_models |
one or more site models, see create_site_models |
tipdates_filename |
name of the file containing tip dates |
tree_prior |
one tree priors, as created by create_tree_prior |
tree_priors |
one or more tree priors, see create_tree_priors |
verbose |
set to TRUE for more output |
This is an internal function, so it should be marked with
@noRd
. This is not done, as this will disallow all
functions to find the documentation parameters
Richèl J.C. Bilderbeek
Get the alignment IDs from one or more 'BEAST2' XML input files.
get_alignment_ids_from_xml(xml_filename)
get_alignment_ids_from_xml(xml_filename)
xml_filename |
name of a 'BEAST2' XML input file. |
a character vector with one or more alignment IDs.
Richèl J.C. Bilderbeek
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() alignment_ids <- get_alignment_ids_from_xml( get_babette_path("anthus_2_4.xml") ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() alignment_ids <- get_alignment_ids_from_xml( get_babette_path("anthus_2_4.xml") ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
inst/extdata
folderGet the full path of a file in the inst/extdata
folder
get_babette_path(filename)
get_babette_path(filename)
filename |
the file's name, without the path |
the full path of the filename, if and only if the file is present. Will stop otherwise.
Richèl J.C. Bilderbeek
for more files, use get_babette_paths
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() get_babette_path("anthus_aco.fas") beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() get_babette_path("anthus_aco.fas") beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
inst/extdata
folderGet the full paths of files in the inst/extdata
folder
get_babette_paths(filenames)
get_babette_paths(filenames)
filenames |
the files' names, without the path |
the filenames' full paths, if and only if all files are present. Will stop otherwise.
Richèl J.C. Bilderbeek
for one file, use get_babette_path
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() get_babette_paths(c("anthus_aco.fas", "anthus_nd2.fas")) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() get_babette_paths(c("anthus_aco.fas", "anthus_nd2.fas")) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
Process the 'BEAST2' output dependent on 'BEAST2' package specifics
parse_beast2_output(out, inference_model)
parse_beast2_output(out, inference_model)
out |
a list with the complete babette output, with elements:
|
inference_model |
a Bayesian phylogenetic inference model, as returned by create_inference_model |
complete babette output with added attributes, which depends on the 'BEAST2' package.
marg_log_lik
the marginal log likelihood estimate
marg_log_lik_sd
the standard deviation around the estimate
estimates
the parameter estimates
created during the marginal likelihood estimation
trees
the trees
created during the marginal likelihood estimation
Richèl J.C. Bilderbeek
Parse the BEAST2 output when run with the BEAST2 NS ('Nested Sampling') package.
parse_beast2_output_to_ns(output)
parse_beast2_output_to_ns(output)
output |
screen output |
a list with the following elements:
marg_log_lik
the marginal log likelihood estimate
marg_log_lik_sd
the standard deviation around the estimate
Richèl J.C. Bilderbeek
use create_test_ns_output
to obtain
a test screen output.
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() parse_beast2_output_to_ns( output = create_test_ns_output() ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() parse_beast2_output_to_ns( output = create_test_ns_output() ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
Draw multiple trees on top of one another.
plot_densitree(phylos, ...)
plot_densitree(phylos, ...)
phylos |
one or more phylogenies, must be of class |
... |
options to be passed to |
nothing. Will produce a plot.
Richèl J.C. Bilderbeek
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() inference_model <- create_test_inference_model() beast2_options <- create_beast2_options() out <- bbt_run_from_model( get_babette_path("anthus_aco.fas"), inference_model = inference_model, beast2_options = beast2_options ) bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) plot_densitree(out$anthus_aco_trees) # Clean up temporary files created by babette bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
if (beautier::is_on_ci() && is_beast2_installed()) { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() inference_model <- create_test_inference_model() beast2_options <- create_beast2_options() out <- bbt_run_from_model( get_babette_path("anthus_aco.fas"), inference_model = inference_model, beast2_options = beast2_options ) bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) plot_densitree(out$anthus_aco_trees) # Clean up temporary files created by babette bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
The inference model and 'BEAST2' options contain paths that may point to sub-sub-sub folders. Create those folders and test if these folders can be written to
prepare_file_creation(inference_model, beast2_options)
prepare_file_creation(inference_model, beast2_options)
inference_model |
a Bayesian phylogenetic inference model, as returned by create_inference_model |
beast2_options |
'BEAST2' options, as can be created by create_beast2_options |
Nothing.
# This example will fail on the CRAN # r-oldrel-macos-x86_64 platform if (rappdirs::app_dir()$os != "mac") { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # For a test inference model, the files can be prepared inference_model <- create_test_inference_model() beast2_options <- create_beast2_options() prepare_file_creation(inference_model, beast2_options) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
# This example will fail on the CRAN # r-oldrel-macos-x86_64 platform if (rappdirs::app_dir()$os != "mac") { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() # For a test inference model, the files can be prepared inference_model <- create_test_inference_model() beast2_options <- create_beast2_options() prepare_file_creation(inference_model, beast2_options) beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }
Update all babette dependencies, by installing their latest versions.
update_babette(upgrade = "default")
update_babette(upgrade = "default")
upgrade |
Deprecated. |
See https://github.com/richelbilderbeek/babetteinstall how to do this.
Nothing.
Giovanni Laudanno, Richèl J.C. Bilderbeek