niche_bars: PNG bar figures to represent ecological niches of distinct...

In nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty

PNG bar figures to represent ecological niches of distinct taxa

Description

niche_bars produces bar plots that represent species ecological niches in one environmental variable. Bars are exported as png figures to an output directory for posterior use.

Usage

niche_bars(tree, whole_rec_table, present = "1", unknown = "?",
           present_col = "#e41a1c", unknown_col = "#969696",
           absent_col = "#377eb8", width = 50, height = 5, res = 300,
           output_directory, overwrite = FALSE)

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.
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	(numeric) width of the device in mm to be passed to the png function. Default = 50.
height	(numeric) height of the device in mm to be passed to the png function. Default = 5.
res	(numeric) nominal resolution in ppi to be passed to the png function. Default = 300.
output_directory	(character) name of the folder in which results will be written. The directory will be created as part of the process.
overwrite	(logical) whether or not to overwrite existing results in output_directory. Default = FALSE.

Details

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 left part of the bar, and the opposite part of the bar represents higher values.

Value

A folder named as in output_directory containing all bar figures produced, as well as a legend to describe what is plotted.

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))

# the running (before running, define a working directory)
niche_bars(tree5, rec_tab, output_directory = file.path(tempdir(), "nichebars"))

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