enmpa (version 0.2.1)

niche_signal: Niche Signal detection using one or multiple variables

Description

Identifies whether a signal of niche can be detected using one or multiple variables. This is an implementation of the methods developed by Cobos & Peterson (2022) doi:10.17161/bi.v17i.15985 that focuses on identifying niche signals in presence-absence data.

Usage

niche_signal(data, condition, variables, method = "univariate",
             permanova_method = "mahalanobis", iterations = 1000,
             set_seed = 1, verbose = TRUE, ...)
niche_signal_univariate(data, condition, variable, iterations = 1000,
                        set_seed = 1, verbose = TRUE)
niche_signal_permanova(data, condition, variables, permutations = 999,
                       permanova_method = "mahalanobis", verbose = TRUE, ...)

Value

A list with results from analysis depending on method.

Arguments

data

matrix or data.frame containing at least the following information: a column representing condition (positive = 1 or negative = 0), and one or more columns representing environmental variables.

condition

(character) name of the column with numeric information about detection (positive = 1 or negative = 0).

variables

(character) vector of one or more names of columns to be used as environmental variables. If method = "univariate", only one variable is used; for method = "permanova", multiple variables can be used.

method

(character) name of the method to be used for niche comparison. Default = "univariate".

permanova_method

(character) name of the dissimilarity index to be used as method in adonis2. See all options in vegdist. Default = "mahalanobis".

iterations

(numeric) number of iterations to be used in analysis. Default = 1000. If method = "permanova", permutations = iterations - 1.

set_seed

(numeric) integer value to specify a initial seed. Default = 1.

verbose

(logical) whether or not to print messages about the process. Default = TRUE.

...

other arguments to be passed to adonis2.

variable

(character) name of the column containing data to be used as environmental variable.

permutations

number of permutations to be performed.

Examples

# Load species occurrences and environmental data.
data("enm_data", package = "enmpa")
head(enm_data)

# Detection of niche signal using an univariate non-parametric test
sn_bio1 <- niche_signal(data = enm_data, variables = "bio_1",
                        condition = "Sp", method = "univariate")
sn_bio1

sn_bio12 <- niche_signal(data = enm_data, variables = "bio_12",
                         condition = "Sp", method = "univariate")
sn_bio12