nichevol_labels {nichevol}R Documentation

Labels to represent changes of niche characteristics between ancestors and descendants

Description

nichevol_labels helps in adding bar-type labels that represent how species' niches changed from ancestors to descendants.

Usage

nichevol_labels(tree, whole_rec_table, ancestor_line = FALSE,
  present = "1", absent = "0", unknown = "?",
  present_col = "#252525", unknown_col = "#d9d9d9",
  no_change_col = "#b2df8a", retraction_col = "#984ea3",
  expansion_col = "#4daf4a", width = 1, height = 1)

Arguments

tree

an object of class "phylo".

whole_rec_table

matrix of reconstructed bins for nodes and species derived from a process of maximum parsimony or maximum likelihood reconstruction. See functions bin_par_rec or bin_ml_rec.

ancestor_line

controls whether ancestor line is plotted. Default = FALSE.

present

(character) code indicating environmental bins in which the species is present. Default = "1".

absent

(character) code indicating environmental bins in which the species is absent. Default = "0".

unknown

(character) code indicating environmental bins in which the species presence is unknown (uncertain). Default = "?".

present_col

color for line representing environments where the species is present. Default = "#252525".

unknown_col

color for line representing environments where the species presence is unknown (uncertain). Default = "#d9d9d9".

no_change_col

color for area of the bar representing environments where no change has been detected. Default = "#b2df8a".

retraction_col

color for area of the bar representing environments where niche retraction has been detected. Default = "#984ea3".

expansion_col

color for area of the bar representing environments where niche expansion has been detected. Default = "#4daf4a".

width

value defining the width of bars representing changes in niches; default = 1.

height

value defining the height of bars representing changes in niches; 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.

Evolution of ecological niches is represented in one environmental dimension, with vertical bars indicating if the niche of the descendant has expanded, retracted, or has not changed compared to its ancestor's niche. Lower values of environmental variables are represented in the lower part of the bar, and the opposite part of the bar represents higher values.

Changes in niches (evolution) are defined as follows:

If ancestor_line is TRUE, the ancestor line will be plotted on the bar representing niche evolution. The line will represent where, in the range of environmental conditions, the ancestor was present, and where its presence is uncertain (unknown).

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)
nichevol_labels(tree5, rec_tab, height = 0.6)
[Package nichevol version 0.1.20 Index]