Examples

Example data and XML files can be examined and run through the import_example function. The examples are numbered 1-4. To access the first set of example files, run:

import_example(1)

This will create a directory pfa_example_1 in your working directory and populate it with the relevant files. The files associated with Example 1 are aquilegia_continuous.csv containing the trait data, aquilegia_newick.txt containing the phylogenetic tree, and example_1.xml containing the instructions for running PFA. To run this example, enter

pfa("pfa_example_1/example_1.xml")

The table below provides a quick summary of the instructions provided in each example XML file.