default_params_doc: This function does nothing. It is intended to inherit is...

In richelbilderbeek/peregrine: Work With The Groninger Peregrine Computer Cluster

This function does nothing. It is intended to inherit is parameters' documentation.

Description

This function does nothing. It is intended to inherit is parameters' documentation.

Usage

default_params_doc(
  alignment,
  alignment_params,
  beast2_options,
  beast2_working_dir,
  chain_length,
  clock_model,
  clock_models,
  crown_age,
  error_measure_params,
  evidence_filename,
  exclude_model,
  experiment,
  experiments,
  experiment_type,
  fasta_filename,
  fileext,
  filename,
  folder_name,
  inference_model,
  input_filename,
  mcmc,
  mcmc_chain_length,
  method,
  misc_params,
  mrca_prior,
  mutation_rate,
  n_replicates,
  output_log_filename,
  output_trees_filenames,
  output_state_filename,
  parameter_filename,
  parameters_filename,
  pattern,
  pff_tmpdir,
  phylo,
  pir_params,
  posterior_trees,
  rng_seed,
  rng_seed_twin_alignment,
  rng_seed_twin_tree,
  root_sequence,
  sample_interval,
  seed,
  sequence_length,
  sim_tral_fun,
  site_model,
  site_models,
  sub_chain_length,
  tree,
  tree_prior,
  tree_priors,
  tree_filename,
  trees_filename,
  twin_alignment_filename,
  twin_evidence_filename,
  twin_model,
  twin_tree_filename,
  twinning_params,
  user_name,
  verbose
)

Arguments

alignment	a DNA alignment
alignment_params	parameters for creating an alignment, as can be created by create_alignment_params
beast2_options	BEAST2 options, as can be created by create_beast2_options
beast2_working_dir	BEAST2 temporary working directory, as used in create_beast2_options
chain_length	something
clock_model	a clock model, as created by create_clock_model
clock_models	a list of one or more clock models, as created by create_clock_model
crown_age	The crown age of the tree.
error_measure_params	parameters to set how the error between given tree and inferred trees in measure, as can be created by create_error_measure_params
evidence_filename	filename to store the estimated evidences (aka marginal likelihoods)
exclude_model	an inference model that has to be excluded, as can be created by create_inference_model
experiment	a pirouette experiment, as can be created by create_experiment
experiments	a list of one or more pirouette experiments, as can be created by create_experiment. If more than one experiment is provided and a "generative" experiment is part of them, the "generative" one has to be the first in the list.
experiment_type	the type of experiment, can be either test or full
fasta_filename	name of a FASTA file
fileext	see tempfile
filename	the file's name, without the path
folder_name	name of the main folder
inference_model	a BEAST2 inference model, as created by create_inference_model
input_filename	BEAST2 input file name, as used in create_beast2_options
mcmc	an MCMC, as created by create_mcmc or by create_pff_mcmc for automatic peregrine friendly filenames check
mcmc_chain_length	length of an MCMC
method	determines how to create the twin tree 'random_tree' just produces a random tree; 'max_clade_cred' simulates n_replicates trees and uses maxCladeCred to create a consensus tree; 'max_likelihood' simulates n_replicates trees and selects the most likely;
misc_params	additional parameters for razzo. They contain tree_filename to store the original given tree and mbd_sim_rng_seed for when an mbd tree is simulated
mrca_prior	an MRCA priors, as created by create_mrca_prior
mutation_rate	something
n_replicates	number of replicates
output_log_filename	BEAST2 ouput .log file name, as used in create_beast2_options
output_trees_filenames	BEAST2 ouput .trees file name, as used in create_beast2_options
output_state_filename	BEAST2 ouput .xml.state file name, as used in create_beast2_options
parameter_filename	full path to a parameters.RDa file
parameters_filename	full path to a parameters.RDa file
pattern	see tempfile
pff_tmpdir	Peregrine-friendly temporary directory name, see get_pff_tempdir
phylo	a phylogeny
pir_params	pirouette parameters, as created by create_pir_params
posterior_trees	phylogenetic trees in a BEAST2 posterior, of class multiphylo
rng_seed	a random number generator seed
rng_seed_twin_alignment	the random number generator seed as used in the simulation of a twin alignment
rng_seed_twin_tree	the random number generator seed as used in the simulation of a twin tree
root_sequence	the DNA sequence at the root of the phylogeny. By default, this will consist out of an equal amount of each letter
sample_interval	the interval at which the MCMC algorithm makes a measurement
seed	a random number generator seed
sequence_length	the length of each DNA sequence in an alignment
sim_tral_fun	function to simulate a true alignment with. This function must have two arguments, called true_phylogeny (which will hold the true phylogeny) and root_sequence (which holds the DNA root sequence). The return type must be DNAbin. Use check_sim_tral_fun to verify if the function has the right signature and output.
site_model	a nucleotide substitution model, as created by create_site_model
site_models	a list of one or more site models, as created by create_site_model
sub_chain_length	length of the sub-chain used by the Nested Sampling algorithm to estimate the marginal likelihood
tree	an ultrametric phylogenetic tree of class phylo
tree_prior	a tree prior, as created by create_tree_prior
tree_priors	a list of one or more tree priors, as created by create_tree_prior
tree_filename	name of the phylogeny file
trees_filename	name of the BEAST2 posterior phylogenies file
twin_alignment_filename	name of the FASTA file the twin alignment will be saved to
twin_evidence_filename	filename to store the estimated evidences (aka marginal likelihoods) of the twin tree
twin_model	the model you want to use to generate the twin tree: birth_death: birth death yule: Yule or pure-birth See get_twin_models to see all possible values of twin_model
twin_tree_filename	name of the (.newick) file the twin tree will be saved to
twinning_params	parameters for creating a twin tree, as can be created by create_twinning_params
user_name	the Peregrine username, for example p123456
verbose	give more output

Note

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

Author(s)

Documentation by Giovanni Laudanno, use of this function by Richel J.C. Bilderbeek

richelbilderbeek/peregrine documentation built on Jan. 3, 2024, 7:42 p.m.