sfreemap.read_tips: Read the tip states and labels from a file
In dpasqualin/sfreemapr: Simulation-Free Stochastic Mapping

Description Usage Arguments Details Value Author(s)

Read a CSV file given as argument and return a matrix representing the states of the tips and its labels (taxa names).

The CSV file must be in a specific format. The first column contain the taxa names, each one in a different row. Every subsequent column is a character, and the state of the character is specified by each taxa on each row, forming a matrix.

You can have as many characters (columns) as you want, but you must specify one to be read, using the character argument, which is an integer representing the column of the character (first character is in column 1).

When some taxon have an ambiguous state, put all states side-by-side, without an separator. For instance, if taxa X can be at both states 'a' and 'b', write 'ab' in the file.

1	sfreemapr.read_tips(file, character=1, sep="\t")

`file`	The path to the file containing the data.
`character`	If the file contains more than one character, you can specify which one to read by the column index.
`sep`	The csv separator, defaults to TAB.

If you decide to use spaces to separate taxa names from characters make sure the taxa names doesn't have spaces. For instance: “A_grahamae_Agra_Cur” is correct, “A grahamae Agra Cur” is wrong.

A matrix with the taxa label as the row names and a number of columns equal to the number of possible states of the character. The values of the matrix can be one, when the taxon can be at the state, and 0 otherwize.

Diego Pasqualin dpasqualin@inf.ufpr.br

dpasqualin/sfreemapr documentation built on May 15, 2019, 10:45 a.m.