set_uncertainty: Set values of uncertainty towards one or both ends of the...

In nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty

Set values of uncertainty towards one or both ends of the variable

Description

set_uncertainty allows to define uncertainty ("?") values around values denoting presence ("1") towards one or both ends of the variable in a table of binary characters.

Usage

set_uncertainty(character_table, species, end)

Arguments

character_table	a matrix of characters to represent ecological niches of the species of interest. A matrix containing values "1" = presence, "0" = absence, and "?" = uncertain. See bin_table.
species	(character) name of the species in the table for which values of uncertainty will be set.
end	(character) end towards which uncertainty values ("?") will be set. Options are: "high", "low", or "both".

Details

Values of characters around those denoting presence ("1") are manually transformed to uncertain ("?") to help producing more conservative reconstructions of ancestral ecological niches. This increases uncertainty in reconstructions and further niche comparisons, which reduces the events of niche change that can be detected. This may be especially useful when dealing with species with one or just a few known records.

Value

A modified matrix of characters to represent ecological niches of the species of interest.

Potential values for characters are:

• "1" = the species is present in those environmental conditions.

• "0" = the species is not present in those environmental conditions. This is, those environmental conditions inside the accessible area (M) are more extreme than the ones used for the species.

• "?" = there is no certainty about the species presence in those environmental conditions.

Examples

# a character table
data("character_table", package = "nichevol")

character_table[, 20:28]

# set values of uncertainty towards the lower end of the variable for species t3
char_tableu <- set_uncertainty(character_table, species = "t2", end = "low")

char_tableu[, 20:28]

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