default_params_doc {mcbette} | R Documentation |
Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.
default_params_doc(
beast2_bin_path,
beast2_folder,
beast2_working_dir,
beast2_options,
beast2_optionses,
clock_model,
clock_models,
epsilon,
fasta_filename,
inference_model,
inference_models,
marg_liks,
mcbette_state,
mcmc,
os,
rng_seed,
site_model,
site_models,
tree_prior,
tree_priors,
verbose
)
beast2_bin_path |
path to the the BEAST2 binary file |
beast2_folder |
the folder where the BEAST2 is installed. Note that this is not the folder where the BEAST2 executable is installed: the BEAST2 executable is in a subfolder. Use get_default_beast2_folder to get the default BEAST2 folder. Use get_default_beast2_bin_path to get the full path to the default BEAST2 executable. Use get_default_beast2_jar_path to get the full path to the default BEAST2 jar file. |
beast2_working_dir |
folder in which BEAST2 will run and produce intermediate files. By default, this is a temporary folder |
beast2_options |
a |
beast2_optionses |
list of one or more |
clock_model |
a clock model, as can be created by create_clock_model |
clock_models |
a list of one or more clock models, as can be created by create_clock_models |
epsilon |
measure of relative accuracy. Smaller values result in longer, more precise estimations |
fasta_filename |
name of the FASTA file |
inference_model |
an inference model, as can be created by create_inference_model |
inference_models |
a list of one or more inference models, as can be created by create_inference_model |
marg_liks |
a table of (estimated) marginal likelihoods, as, for example, created by est_marg_liks. This data.frame has the following columns:
Use get_test_marg_liks to get a test |
mcbette_state |
the mcbette state, which is a list with the following elements: |
mcmc |
an MCMC for the Nested Sampling run, as can be created by create_mcmc_nested_sampling |
os |
name of the operating system,
must be |
rng_seed |
a random number generator seed used for the BEAST2 inference |
site_model |
a site model, as can be created by create_site_model |
site_models |
a list of one or more site models, as can be created by create_site_models |
tree_prior |
a tree prior, as can be created by create_tree_prior |
tree_priors |
a list of one or more tree priors, as can be created by create_tree_priors |
verbose |
if TRUE show debug output |
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
Richèl J.C. Bilderbeek