default_params_doc {beautier}  R Documentation 
Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.
Description
Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.
Usage
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
)
Arguments
alignment_id 
ID of the alignment,
as returned by get_alignment_id.
Keep at 
allow_empty_str 
allow a string to be empty 
allow_na 
allow NA 
alpha_parameter 
an alpha parameter, as created by create_alpha_param 
b_pop_sizes_param 
a Bayesian population size parameter, as created by create_b_pop_sizes_param 
b_pop_sizes_parameter 
a Bayesian population size parameter, as created by create_b_pop_sizes_param 
bd_tree_prior 
a BirthDeath tree prior, as created
by 
beautier_folder 
the path to the beautier temporary files folder 
cbs_tree_prior 
a Coalescent Bayesian Skyline tree prior,
as returned by 
beast2_version 
BEAST2 version, for example, 
beauti_options 
one BEAUti options object,
as returned by 
beta_parameter 
a beta parameter, as created by create_beta_param 
ccp_tree_prior 
a Coalescent Constant Population tree prior,
as returned by 
cep_tree_prior 
a Coalescent Exponential Population tree prior,
as returned by 
chain_length 
length of the MCMC chain 
clock_model 
a clock model,
as returned by 
clock_model_name 
name of a clock model,
must be a name as returned by 
clock_model_names 
one or more names of a clock model,
must be name among those returned by 
clock_models 
a list of one or more clock models,
as returned by 
clock_prior_distr_id 
ID of an MRCA clock model's distribution.
Keep at 
clock_rate_param 
a 
crown_age 
the crown age of the phylogeny 
crown_ages 
the crown ages of the phylogenies. Set to NA if the crown age needs to be estimated 
distr_id 
a distributions' ID 
fasta_filename 
a FASTA filename.
Use 
fasta_filenames 
One or more FASTA filenames.
Use 
filename 
a filename, as can be checked by check_filename 
fixed_crown_age 
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. 
fixed_crown_ages 
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. 
freq_param 
a 'freq' parameter, as created by create_freq_param 
gamma_distr 
a gamma distribution,
as created by 
gamma_site_model 
a site model's gamma site model,
as returned by 
group_sizes_dimension 
the group sizes' dimension,
as used by the CBS tree prior (see 
gtr_site_model 
a GTR site model,
as returned by 
has_non_strict_clock_model 
boolean to indicate that the is already at least one nonstrict (i.e. relaxed lognormal) clock model 
has_tip_dating 
TRUE if the user has supplied tip dates, FALSE otherwise 
hky_site_model 
an HKY site model,
as returned by 
id 
an alignment's IDs.
An ID can be extracted from its FASTA filename
with 
ids 
one or more alignments' IDs.
IDs can be extracted from their FASTA filenames
with 
inference_model 
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. 
inference_models 
a list of one or more inference models, as can be created by create_inference_model 
initial_phylogenies 
one or more MCMC chain's initial phylogenies.
Each one set to 
input_filename 
A FASTA filename.
Use 
input_filenames 
One or more FASTA filenames.
Use 
is_monophyletic 
boolean to indicate monophyly is assumed in
a Most Recent Common Ancestor prior,
as returned by 
jc69_site_model 
a JC69 site model,
as returned by 
kappa_param 
a kappa parameter, as created by create_kappa_param 
log_every 
number of MCMC states between writing to file 
m_param 
an m parameter, as created by create_m_param 
mcmc 
one MCMC.
Use 
mode 
mode how to log. Valid values are the ones returned by get_log_modes 
mrca_prior 
a Most Recent Common Ancestor prior,
as returned by 
mrca_priors 
a list of one or more Most Recent Common Ancestor priors,
as returned by 
mrca_prior_name 
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. 
n_init_attempts 
number of initialization attempts before failing 
output_filename 
Name of the XML parameter file created by this function. BEAST2 uses this file as input. 
param 
a parameter, as can be created by 
param_id 
a parameter's ID 
phylogeny 
a phylogeny of type 
pop_sizes_scaler_scale_factor 
the scale factor used by the population sizes scaler operator 
pre_burnin 
number of burn in samples taken before entering the main loop 
rate_scaler_factor 
the strict clock model's operator scaler for the rate. Use an empty string to indicate the default. 
rename_fun 
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:

rln_clock_model 
a Relaxed LogNormal clock model,
as returned by 
sample_from_prior 
set to TRUE to sample from the prior 
sanitise_headers 
set to TRUE to sanitise the headers of the log file 
screenlog 
a 
sequence_length 
a DNA sequence length, in base pairs 
site_model 
a site model,
as returned by 
site_model_name 
name of a site model,
must be a name as returned by 
site_model_names 
one or more names of a site model,
must be name among those returned by 
site_models 
one or more site models,
as returned by 
sort 
how to sort the log. Valid values are the ones returned by get_log_sorts 
store_every 
number of states the MCMC will process
before the posterior's state will be saved to file.
Use 1 or 
strict_clock_model 
a strict clock model,
as returned by 
taxa_names 
names of the taxa,
as returned by 
tipdates_filename 
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. 
tn93_site_model 
a TN93 site model,
as returned by 
tracelog 
a 
treelog 
a 
tree_prior 
a tree priors,
as returned by 
tree_prior_name 
name of a tree prior,
must be a name as returned by 
tree_prior_names 
one or more names of a tree prior,
must be a name among those returned by 
tree_priors 
one or more tree priors,
as returned by 
verbose 
if TRUE, additional information is displayed, that is potentially useful in debugging 
yule_tree_prior 
a Yule tree_prior,
as created by 
Note
This is an internal function, so it should be marked with
@export
. This is not done, as this will disallow all
functions to find the documentation parameters
Author(s)
RichÃ¨l J.C. Bilderbeek