read.p4d {phylosignal} | R Documentation |
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
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 " |
data.format |
the format of the table with tips data.
Possible formats are " |
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 functionread.tree
of the ape package.The
nexus
format refers to NEXUS format. The tree is read by calling the functionread.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
useread.table
with default settings. -
csv
useread.csv
with default settings. -
csv2
useread.csv2
with default settings. -
delim
useread.delim
with default settings. -
delim2
useread.delim2
with default settings.
Value
An object of class phylo4d
.
See Also
phylo4d
to create a phylo4d
object.