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

Description Usage Arguments Note Author(s)

View source: R/default_params_doc.R

Description

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

Usage

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default_params_doc(
  alignment,
  alignment_params,
  bd_mutation_rate,
  bd_tree,
  bd_tree_filename,
  bins,
  brts,
  chain_length,
  clock_model,
  cond,
  crown_age,
  error_measure_params,
  experiment_type,
  experiments,
  fasta_filename,
  filename,
  folder_name,
  init_speciation_rate,
  init_extinction_rate,
  lambda,
  lambdas,
  mbd_l_matrix,
  mbd_mutation_rate,
  mbd_params,
  mbd_paramses,
  mbd_params_interval,
  mbd_sim_rng_seed,
  mbd_tree,
  mcmc_chain_length,
  misc_params,
  model_type,
  mu,
  mus,
  mutation_rate,
  n_replicates,
  nu,
  nus,
  nu_events,
  parameters,
  parameter_filename,
  parameters_filename,
  phylo,
  pir_params,
  posterior_trees,
  precision,
  project_folder_name,
  q,
  qs,
  razzo_params,
  razzo_paramses,
  rng_seed,
  sample_interval,
  seed,
  seed_folder,
  sequence_length,
  sim_pars,
  sim_phylo,
  site_model,
  sub_chain_length,
  tree,
  tree_type,
  tree_filename,
  trees_filename,
  twinning_params,
  verbose
)

Arguments

alignment

a DNA alignment

alignment_params

parameters for creating an alignment, as can be created by create_alignment_params

bd_mutation_rate

the mutation rate when creating an alignment from a BD tree

bd_tree

a phylogent of class phylo, created by a Birth Death process

bd_tree_filename

name of the file that stores a BD twin tree

bins

how many bins in the histograms?

brts

set of branching times

chain_length

something

clock_model

Name of the clock model that has to be used for the inference. Valid names are 'strict' and 'rln'.

cond

conditioning as specified in mbd_sim

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

experiment_type

the type of experiment, can be either test or full

experiments

provides information on how the experiment has to be set up. To create it use create_experiment

fasta_filename

name of a FASTA file

filename

the file's name, without the path

folder_name

name of the main folder

init_speciation_rate

a speciation rate

init_extinction_rate

an extinction rate

lambda

per-lineage speciation rate. See mbd_sim

lambdas

per-lineage speciation rates. See mbd_sim

mbd_l_matrix

the L matrix of an MBD tree

mbd_mutation_rate

the mutation rate when creating an alignment from a MBD tree

mbd_params

MBD parameter set

mbd_paramses

data frame with one MBD parameter set per row. If a simulation with one MBD parameter set has 10 replicates, this data frame will hold 10 rows, each with different seeds

mbd_params_interval

data frame with one MBD parameter set per row. If a simulation with one MBD parameter set has 10 replicates, this data frame will hold 10 rows, each with different seeds

mbd_sim_rng_seed

rng seed to simulate a mbd tree

mbd_tree

an MBD tree

mcmc_chain_length

length of an MCMC

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

model_type

the type of inference model, must be generative or candidate

mu

per-species extinction rate. See mbd_sim

mus

per-species extinction rates. See mbd_sim

mutation_rate

something

n_replicates

number of replicates

nu

the rate at which a multiple-birth specation is triggered. See mbd_sim

nus

the rates at which a multiple-birth specation is triggered. See mbd_sim

nu_events

the number of nu-triggered events that have to be present in the simulated tree

parameters

the razzo parameters

parameter_filename

full path to a parameters.RDa file

parameters_filename

full path to a parameters.RDa file

phylo

a phylogeny

pir_params

a parameter set for one pirouette run, as created by create_pir_params. Use create_test_razzo_pir_params to create a pir_params that has the file naming scheme as razzo

posterior_trees

phylogenetic trees in a BEAST2 posterior, of class multiphylo

precision

define the precision of the approximation.

project_folder_name

project folder name, will be the full path to razzo_project

q

per-species speciation probability in case of occurrance of a multiple event. See mbd_sim

qs

per-species speciation probabilities in case of occurrance of a multiple event. See mbd_sim

razzo_params

a parameter set for one razzo experiment, as created by create_params_razzo and used by run_razzo

razzo_paramses

a list of razzo_params for a set of razzo experiment. Use create create_razzo_paramses or create_test_razzo_paramses to create such a list

rng_seed

a random number generator seed

sample_interval

the interval at which the MCMC algorithm makes a measurement

seed

a random number generator seed

seed_folder

the folder where the data for a specific seed is stored

sequence_length

the length of each DNA sequence in an alignment

sim_pars

something

sim_phylo

something

site_model

Name of the site model that has to be used for the inference. Valid names are 'jc69' and 'gtr'.

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_type

can be 'true' or 'twin'

tree_filename

name of the phylogeny file

trees_filename

name of the BEAST2 posterior phylogenies file

twinning_params

parameters for creating a twin tree, as can be created by create_twinning_params

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/razzo documentation built on March 10, 2021, 1:17 p.m.