save_parameters_to_file: Creates a valid parameter file

In richelbilderbeek/wiritttes: WIRITTE simulation

Description

Creates a valid parameter file

Usage

save_parameters_to_file(rng_seed, sirg, siri, scr, erg, eri, age, mutation_rate,
  n_alignments, sequence_length, nspp, n_beast_runs, filename,
  fixed_crown_age = FALSE)

Arguments

rng_seed	the random number generator seed
sirg	the species initiation rate of the good species
siri	the speciation-initiation rate of the incipient species
scr	the rate at which incipient species become good
erg	the rate at which good species get extinct
eri	the rate at which incipient species get extinct
age	crown age of the phylogeny
mutation_rate	the probability per nucleotide to mutate at a DNA replication
n_alignments	the number of alignments simulated per species tree
sequence_length	the simulated DNA sequence length in nucleotides
nspp	the number of states in the MCMC chain that BEAST2 will run
n_beast_runs	the number of BEAST2 runs per DNA alignments
filename	the name of the parameter file that will be created by this function
fixed_crown_age	the crown age is fixed (for TRUE) or estimated with lambda and mu (for FALSE)

Value

Nothing, it will create a file with filename 'filename'

Author(s)

Richel Bilderbeek

Examples

filename <- "save_parameters_to_file_example.RDa"
save_parameters_to_file(
  rng_seed = 42,
  sirg = 0.5,
  siri = 0.5,
  scr = 0.5,
  erg = 0.5,
  eri = 0.5,
  age = 5,
  mutation_rate = 0.1,
  n_alignments = 1,
  sequence_length = 10,
  nspp = 10,
  n_beast_runs = 1,
  filename = filename
)
testit::assert(is_valid_file(filename) == TRUE)

richelbilderbeek/wiritttes documentation built on May 27, 2019, 8:14 a.m.