Read a phylo4d object from files

Description

This function creates an object of class phylo4d by combining a phylogenetic tree and its associated tips data stored in two distinct files.

Usage

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read.p4d(phylo.file, data.file, phylo.format = "newick",
  data.format = "table")

Arguments

phylo.file

the name of the file which the phylogenetic tree is to be read from.

data.file

the name of the file which the tips data are to be read from.

phylo.format

the format of the phylogenetic tree provided. Possible formats are "newick" and "nexus".

data.format

the format of the table with tips data. Possible formats are "table", "csv", "csv2", "delim" and "delim2".

Details

phylo.file and data.file can be provided as objects of mode character or double-quoted strings.

The phylogenetic tree can be imported in two formats.

  • The newick format refers to the simple parenthetic format known as the Newick or New Hampshire format. The tree is read by calling the function read.tree of the ape package.

  • The nexus format refers to NEXUS format. The tree is read by calling the function read.nexus of the ape package.

Tips data are imported from a table formatted file. The different formats allow to use different separator and decimal characters. They correspond to the variants of read.table:

  • table use read.table with default settings.

  • csv use read.csv with default settings.

  • csv2 use read.csv2 with default settings.

  • delim use read.delim with default settings.

  • delim2 use read.delim2 with default settings.

Value

An object of class phylo4d.

See Also

phylo4d to create a phylo4d object.

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