makeInfile: makeInfile Takes a tree and some data, ladderizes the tree,...

In hferg/BTprocessR: A set of tools to help with the interpretation and analysis of the output of BayesTraits MCMC analyses.

Description

makeInfile Takes a tree and some data, ladderizes the tree, matches the tree and the data and then makes a run file based on a control list. The prepared tree, data, infile and command to execute the analysis will be written out to the analysis_path with the prefixes analysis_name. Sets up basic BayesTraits analysis - for more complex analyses (e.g. alternate priors, parameter restriction, fixed scalars on nodes, fossilised states etc.) users must write their own control files.

Usage

makeInfile(tree, data, analysis_name, analysis_path, species_col = NULL,
  job = FALSE, bt.control = list(), job.control = list())

Arguments

tree	The tree for the analysis to be run on.
data	The data to analyse
analysis_path	The file path to put the resultant files in - defaults to working directory.
analaysis_name	The name for the analysis - will be prefixed to all files generated.
control	List of options for BayesTraits.

hferg/BTprocessR documentation built on March 8, 2020, 11:45 a.m.