niche_labels: Labels to represent niches of tips and ancestors

In nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty

Labels to represent niches of tips and ancestors

Description

niche_labels helps in adding bar-type labels that represent species ecological niches in one environmental variable.

Usage

niche_labels(tree, whole_rec_table, label_type = "tip_node",
             tip_offset = 0.015, present = "1", unknown = "?",
             present_col = "#e41a1c", unknown_col = "#969696",
             absent_col = "#377eb8", width = 1, height = 1)

Arguments

tree	an object of class "phylo".
whole_rec_table	matrix of environmental bins for all tips and nodes derived from functions bin_par_rec or bin_ml_rec.
label_type	(character) type of label; options are: "tip", "node", and "tip_node". Default = "tip_node".
tip_offset	(numeric) space between tips and the labels. Default = 0.015.
present	(character) code indicating environmental bins in which the species is present. Default = "1".
unknown	(character) code indicating environmental bins in which the species presence is unknown (uncertain). Default = "?".
present_col	color for area of the bar representing environments where the species is present. Default = "#e41a1c".
unknown_col	color for area of the bar representing environments where the species presence is unknown (uncertain). Default = "#969696".
absent_col	color for area of the bar representing environments where no change has been detected. Default = "#377eb8".
width	value defining the width of niche bars; default = 1.
height	value defining the height of niche bars; default = 1.

Details

For the moment, only plots of type "phylogram" with "rightwards" or "leftwards" directions, created with the function plot.phylo from the package ape are supported.

Ecological niches are represented in one environmental dimension with vertical bars that indicate if the species is present, absent, or if its presence is uncertain in the range of environmental conditions. Lower values of environmental variables are represented in the lower part of the bar, and the opposite part of the bar represents higher values.

Examples

# a simple tree
data("tree5", package = "nichevol")

# a matrix of niche charactes (1 = present, 0 = absent, ? = unknown)
dataTable <- cbind("241" = rep("1", length(tree5$tip.label)),
                   "242" = rep("1", length(tree5$tip.label)),
                   "243" = c("1", "1", "0", "0", "0"),
                   "244" = c("1", "1", "0", "0", "0"),
                   "245" = c("1", "?", "0", "0", "0"))
rownames(dataTable) <- tree5$tip.label

# list with two objects (tree and character table)
treeWdata <- geiger::treedata(tree5, dataTable)

# Maximum parsimony reconstruction
rec_tab <- smooth_rec(bin_par_rec(treeWdata))

# plotting and adding labels
ape::plot.phylo(tree5, label.offset = 0.04)
niche_labels(tree5, rec_tab, height = 0.6)

nichevol documentation built on March 31, 2023, 5:38 p.m.