selected_sites_DI: Dissimilarity indices from PAM_subset

In claununez/biosurvey: Tools for Biological Survey Planning

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:

• Dissimilarity matrices for all PAMs reduced based on distinct sets of selected sites.

• A matrix summarizing incidences from all sets of selected sites.

• A dissimilarity matrix for the summary of incidences for all sets of selected sites.

• The result of clustering sets of selected sites based on dissimilarities.

Examples

# Data
b_pam <- read_PAM(system.file("extdata/b_pam.rds",
                              package = "biosurvey"))
m_selection <- read_master(system.file("extdata/m_selection.rds",
                                       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)

claununez/biosurvey documentation built on April 25, 2024, 12:24 a.m.