selected_sites_DI {biosurvey}R Documentation

Dissimilarity indices from PAM_subset

Description

Computes dissimilarity indices for each set of selected sites contained in elements of PAM_subset that contain information of species incidence (presence-absence). Calculations are done also among sets of selected sites.

Usage

selected_sites_DI(PAM_subset, selection_type = "all", method = "jaccard",
                  verbose = TRUE, ...)

Arguments

PAM_subset

object of class PAM_subset obtained using the function subset_PAM.

selection_type

type of selection to be considered when creating dissimilarity matrices for elements in PAM_subset. Options are: "all", "random", "E", "G", and "EG". The default, "all", uses all selection types present in PAM_subset.

method

(character) dissimilarity index to be passed to function vegdist. Default = "jaccard". See details.

verbose

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

...

other arguments to be passed to function vegdist.

Details

Important details about the process performed to compute dissimilarity indices can be seen in the documentation of vegdist.

Value

A list containing:

Examples

# Data
data("b_pam", package = "biosurvey")
data("m_selection", package = "biosurvey")

# Subsetting base PAM according to selections
sub_pam_all <- subset_PAM(b_pam, m_selection, selection_type = "all")

# Calculating dissimilarities
DI_sel <- selected_sites_DI(sub_pam_all)

[Package biosurvey version 0.1.1 Index]