Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.

default_params_doc(
  alignment_id,
  alpha_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,
  fixed_crown_age,
  fixed_crown_ages,
  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,
  log_every,
  m_param,
  mcmc,
  mode,
  mrca_prior,
  mrca_priors,
  mrca_prior_name,
  n_init_attempts,
  output_filename,
  param,
  param_id,
  phylogeny,
  pre_burnin,
  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 NA to have it initialized automatically

alpha_parameter

an alpha parameter, as created by create_alpha_param

bd_tree_prior

a Birth-Death tree prior, as created by create_bd_tree_prior

beautier_folder

the path to the beautier temporary files folder

cbs_tree_prior

a Coalescent Bayesian Skyline tree prior, as returned by create_cbs_tree_prior

beast2_version

BEAST2 version, for example, code"2.5"

beauti_options

one BEAUti options object, as returned by create_beauti_options

beta_parameter

a beta parameter, as created by create_beta_param

ccp_tree_prior

a Coalescent Constant Population tree prior, as returned by create_ccp_tree_prior

cep_tree_prior

a Coalescent Exponential Population tree prior, as returned by create_cep_tree_prior

chain_length

length of the MCMC chain

clock_model

a clock model, as returned by create_clock_model

clock_model_name

name of a clock model, must be a name as returned by get_clock_model_names

clock_model_names

one or more names of a clock model, must be name among those returned by get_clock_model_names

clock_models

a list of one or more clock models, as returned by create_clock_model

clock_prior_distr_id

ID of an MRCA clock model's distribution. Keep at NA to have it initialized automatically

clock_rate_param

a clockRate parameter, a numeric value, as created by create_clock_rate_param

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 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.

fasta_filenames

One or more FASTA filenames. Use get_fasta_filename to obtain a testing FASTA 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.

gamma_distr

a gamma distribution, as created by create_gamma_distr)

gamma_site_model

a site model's gamma site model, as returned by create_gamma_site_model

group_sizes_dimension

the group sizes' dimension, as used by the CBS tree prior (see create_cbs_tree_prior)

gtr_site_model

a GTR site model, as returned by create_gtr_site_model

has_non_strict_clock_model

boolean to indicate that the is already at least one non-strict (i.e. relaxed log-normal) 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 create_hky_site_model

id

an alignment's IDs. An ID can be extracted from its FASTA filename with get_alignment_ids_from_fasta_filenames)

ids

one or more alignments' IDs. IDs can be extracted from their FASTA filenames with get_alignment_ids_from_fasta_filenames)

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 NA will result in BEAST2 using a random phylogeny. Else the phylogeny is assumed to be of class phylo from the ape package

input_filename

A FASTA filename. Use get_fasta_filename to obtain a testing FASTA filename.

input_filenames

One or more FASTA filenames. Use get_fasta_filename to obtain a testing FASTA filename.

is_monophyletic

boolean to indicate monophyly is assumed in a Most Recent Common Ancestor prior, as returned by create_mrca_prior

jc69_site_model

a JC69 site model, as returned by create_jc69_site_model

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 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

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 create_mrca_prior

mrca_priors

a list of one or more Most Recent Common Ancestor priors, as returned by create_mrca_prior

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 create_param.

param_id

a parameter's ID

phylogeny

a phylogeny of type phylo from the ape package

pre_burnin

number of burn in samples taken before entering the main loop

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:

  • 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

rln_clock_model

a Relaxed Log-Normal clock model, as returned by create_rln_clock_model

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 screenlog, as created by create_screenlog

sequence_length

a DNA sequence length, in base pairs

site_model

a site model, as returned by create_site_model

site_model_name

name of a site model, must be a name as returned by get_site_model_names

site_model_names

one or more names of a site model, must be name among those returned by get_site_model_names

site_models

one or more site models, as returned by create_site_model

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 NA to use the default frequency.

strict_clock_model

a strict clock model, as returned by create_strict_clock_model

taxa_names

names of the taxa, as returned by get_taxa_names. Keep at NA to have it initialized automatically, using all taxa in the alignment

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 create_tn93_site_model

tracelog

a tracelog, as created by create_tracelog

treelog

a treelog, as created by create_treelog

tree_prior

a tree priors, as returned by create_tree_prior

tree_prior_name

name of a tree prior, must be a name as returned by get_tree_prior_names

tree_prior_names

one or more names of a tree prior, must be a name among those returned by get_tree_prior_names

tree_priors

one or more tree priors, as returned by create_tree_prior

verbose

if TRUE, additional information is displayed, that is potentially useful in debugging

yule_tree_prior

a Yule tree_prior, as created by create_yule_tree_prior

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

Richèl J.C. Bilderbeek