Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.
default_params_doc(
alignment_id,
allow_empty_str,
allow_na,
alpha_parameter,
b_pop_sizes_param,
b_pop_sizes_parameter,
bd_tree_prior,
beautier_folder,
cbs_tree_prior,
beast2_version,
beauti_options,
beta_parameter,
ccp_tree_prior,
cep_tree_prior,
chain_length,
clock_model,
clock_model_name,
clock_model_names,
clock_models,
clock_prior_distr_id,
clock_rate_param,
crown_age,
crown_ages,
distr_id,
fasta_filename,
fasta_filenames,
filename,
fixed_crown_age,
fixed_crown_ages,
freq_param,
gamma_distr,
gamma_site_model,
group_sizes_dimension,
gtr_site_model,
has_non_strict_clock_model,
has_tip_dating,
hky_site_model,
id,
ids,
inference_model,
inference_models,
initial_phylogenies,
input_filename,
input_filenames,
is_monophyletic,
jc69_site_model,
kappa_param,
log_every,
m_param,
mcmc,
mode,
mrca_prior,
mrca_priors,
mrca_prior_name,
n_init_attempts,
output_filename,
param,
param_id,
phylogeny,
pop_sizes_scaler_scale_factor,
pre_burnin,
rate_scaler_factor,
rename_fun,
rln_clock_model,
sample_from_prior,
sanitise_headers,
screenlog,
sequence_length,
site_model,
site_model_name,
site_model_names,
site_models,
sort,
store_every,
strict_clock_model,
taxa_names,
tipdates_filename,
tn93_site_model,
tracelog,
treelog,
tree_prior,
tree_prior_name,
tree_prior_names,
tree_priors,
verbose,
yule_tree_prior
)ID of the alignment,
as returned by get_alignment_id.
Keep at NA to have it initialized automatically
allow a string to be empty
allow NA
an alpha parameter, as created by create_alpha_param
a Bayesian population size parameter, as created by create_b_pop_sizes_param
a Bayesian population size parameter, as created by create_b_pop_sizes_param
a Birth-Death tree prior, as created
by create_bd_tree_prior
the path to the beautier temporary files folder
a Coalescent Bayesian Skyline tree prior,
as returned by create_cbs_tree_prior
BEAST2 version, for example, "2.5"
one BEAUti options object,
as returned by create_beauti_options
a beta parameter, as created by create_beta_param
a Coalescent Constant Population tree prior,
as returned by create_ccp_tree_prior
a Coalescent Exponential Population tree prior,
as returned by create_cep_tree_prior
length of the MCMC chain
a clock model,
as returned by create_clock_model
name of a clock model,
must be a name as returned by get_clock_model_names
one or more names of a clock model,
must be name among those returned by get_clock_model_names
a list of one or more clock models,
as returned by create_clock_model
ID of an MRCA clock model's distribution.
Keep at NA to have it initialized automatically
a clockRate parameter,
a numeric value,
as created by create_clock_rate_param
the crown age of the phylogeny
the crown ages of the phylogenies. Set to NA if the crown age needs to be estimated
a distributions' ID
a FASTA filename.
Use get_fasta_filename to obtain a testing FASTA filename.
Note that BEAST2 also supports missing data,
by using a dash (-) or question mark (?)
as a sequence.
One or more FASTA filenames.
Use get_fasta_filename to obtain a testing FASTA filename.
a filename, as can be checked by check_filename
determines if the phylogeny's crown age is fixed. If FALSE, crown age is estimated by BEAST2. If TRUE, the crown age is fixed to the crown age of the initial phylogeny.
one or more booleans to determine if the phylogenies' crown ages are fixed. If FALSE, crown age is estimated by BEAST2. If TRUE, the crown age is fixed to the crown age of the initial phylogeny.
a `freq` parameter, as created by create_freq_param
a gamma distribution,
as created by create_gamma_distr)
a site model's gamma site model,
as returned by create_gamma_site_model
the group sizes' dimension,
as used by the CBS tree prior (see create_cbs_tree_prior)
a GTR site model,
as returned by create_gtr_site_model
boolean to indicate that the is already at least one non-strict (i.e. relaxed log-normal) clock model
TRUE if the user has supplied tip dates, FALSE otherwise
an HKY site model,
as returned by create_hky_site_model
an alignment's IDs.
An ID can be extracted from its FASTA filename
with get_alignment_ids_from_fasta_filenames)
one or more alignments' IDs.
IDs can be extracted from their FASTA filenames
with get_alignment_ids_from_fasta_filenames)
a Bayesian phylogenetic inference model. An inference model is the complete model setup in which a site model, clock model, tree prior and more are specified. Use create_inference_model to create an inference model. Use check_inference_model to check if an inference model is valid. Use rename_inference_model_filenames to rename the files in an inference model.
a list of one or more inference models, as can be created by create_inference_model
one or more MCMC chain's initial phylogenies.
Each one set to NA will result in BEAST2 using a random phylogeny.
Else the phylogeny is assumed to be of class phylo from the
ape package
A FASTA filename.
Use get_fasta_filename to obtain a testing FASTA filename.
One or more FASTA filenames.
Use get_fasta_filename to obtain a testing FASTA filename.
boolean to indicate monophyly is assumed in
a Most Recent Common Ancestor prior,
as returned by create_mrca_prior
a JC69 site model,
as returned by create_jc69_site_model
a kappa parameter, as created by create_kappa_param
number of MCMC states between writing to file
an m parameter, as created by create_m_param
one MCMC.
Use create_mcmc to create an MCMC.
Use create_ns_mcmc to create an MCMC
for a Nested Sampling run.
Use check_mcmc to check if an MCMC is valid.
Use rename_mcmc_filenames to rename the filenames in an MCMC.
mode how to log. Valid values are the ones returned by get_log_modes
a Most Recent Common Ancestor prior,
as returned by create_mrca_prior
a list of one or more Most Recent Common Ancestor priors,
as returned by create_mrca_prior
the unique name of the MRCA prior, for example a genus, family, order or even class name. Leave at NA to have it named automatically.
number of initialization attempts before failing
Name of the XML parameter file created by this function. BEAST2 uses this file as input.
a parameter, as can be created by create_param.
a parameter's ID
a phylogeny of type phylo from the ape
package
the scale factor used by the population sizes scaler operator
number of burn in samples taken before entering the main loop
the strict clock model's operator scaler for the rate. Use an empty string to indicate the default.
a function to rename a filename, as can be checked by check_rename_fun. This function should have one argument, which will be a filename or NA. The function should return one filename (when passed one filename) or one NA (when passed one NA). Example rename functions are:
get_remove_dir_fun get a function that removes the directory paths from the filenames, in effect turning these into local files
get_replace_dir_fun get a function that replaces the directory paths from the filenames
get_remove_hex_fun get a function that removes the
hex string from filenames.
For example, tracelog_82c1a522040.log becomes tracelog.log
a Relaxed Log-Normal clock model,
as returned by create_rln_clock_model
set to TRUE to sample from the prior
set to TRUE to sanitise the headers of the log file
a screenlog,
as created by create_screenlog
a DNA sequence length, in base pairs
a site model,
as returned by create_site_model
name of a site model,
must be a name as returned by get_site_model_names
one or more names of a site model,
must be name among those returned by get_site_model_names
one or more site models,
as returned by create_site_model
how to sort the log. Valid values are the ones returned by get_log_sorts
number of states the MCMC will process
before the posterior's state will be saved to file.
Use -1 or NA to use the default frequency.
a strict clock model,
as returned by create_strict_clock_model
names of the taxa,
as returned by get_taxa_names.
Keep at NA to have it initialized automatically,
using all taxa in the alignment
name of the file containing the tip dates. This file is assumed to have two columns, separated by a tab. The first column contains the taxa names, the second column contains the date.
a TN93 site model,
as returned by create_tn93_site_model
a tracelog,
as created by create_tracelog
a treelog,
as created by create_treelog
a tree priors,
as returned by create_tree_prior
name of a tree prior,
must be a name as returned by get_tree_prior_names
one or more names of a tree prior,
must be a name among those returned by get_tree_prior_names
one or more tree priors,
as returned by create_tree_prior
if TRUE, additional information is displayed, that is potentially useful in debugging
a Yule tree_prior,
as created by create_yule_tree_prior
Richèl J.C. Bilderbeek