default_params_doc: This function does nothing. It is intended to inherit is...
In richelbilderbeek/raket: What If Speciation Takes Time?

Description Usage Arguments Note Author(s)

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

default_params_doc(alignment_params, crown_age, erg, ergs, eri, eris,
  experiment_type, filename, max_n_params, mcmc, mcmc_chain_length,
  n_replicates, pbd_params, pbd_sim_out_filename, pir_params,
  project_folder_name, quantile, raket_params, raket_paramses,
  sampling_method, scr, scrs, sequence_length, sir, sirg, sirgs, siri,
  siris, stem_age, true_tree_filename, twinning_params, verbose)

`alignment_params`	parameters for creating an alignment, as can be created by `create_alignment_params`
`crown_age`	the crown age of the phylogeny
`erg`	extinction rate of a good species
`ergs`	extinction rates for good species
`eri`	extinction rate of an incipient species
`eris`	extinction rates for incipient species
`experiment_type`	type of experiment, must a member of `rkt_get_experiment_types`
`filename`	name of the file
`max_n_params`	the maximum number of parameters created. Set to a lower value in debugging
`mcmc`	one mcmc object, as returned by `create_mcmc`
`mcmc_chain_length`	length of the MCMC chain, in number of states
`n_replicates`	number of replicates per biological parameter set
`pbd_params`	a PBD parameter set, as returned by `create_pbd_params`
`pbd_sim_out_filename`	path to file to save the PBD simulation's output to. Data will be stored as R Data (`.RDa`).
`pir_params`	`pirouette` parameter set, as created by create_pir_params
`project_folder_name`	name of project folder
`quantile`	the quantile, a value from, and including, zero to one
`raket_params`	`raket` parameters for one experiment, as can be created by `create_raket_params`
`raket_paramses`	a list of `raket_params`, as created by `create_general_params_set` or `create_sampling_params_set`
`sampling_method`	method how the incipient species representing a species is picked. Must be in rkt_get_sampling_methods.
`scr`	speciation completion rate
`scrs`	speciation completion rates
`sequence_length`	a DNA sequence length, in base pairs
`sir`	speciation initiation rate of both a good species and an incipient species
`sirg`	speciation initiation rate of a good species
`sirgs`	speciation initiation rates of good species
`siri`	speciation initiation rate of an incipient species
`siris`	speciation initiation rates of incipient species
`stem_age`	stem age. Set either the stem age or the crown age.
`true_tree_filename`	path to the file to store the true phylogentic tree to. Tree will be stored in Newick format.
`twinning_params`	parameters for creating a twin tree, as can be created by `create_twinning_params`
`verbose`	if TRUE, additional information is displayed, that is potentially useful in debugging

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

Richel J.C. Bilderbeek

richelbilderbeek/raket documentation built on Dec. 31, 2019, 7:41 p.m.