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Attribute-space Presence–Absence Matrix (attrPAM)

Source: R/lets_attrpam.R
lets.attrpam.Rd

Builds a presence–absence matrix (PAM) in a two-dimensional **trait space**, by binning species occurrences along two quantitative attributes (e.g., body size and mass). Each species can have one or multiple entries in the trait dataset.

Usage

lets.attrpam(
  x,
  n_bins = 10,
  remove.cells = TRUE,
  remove.sp = TRUE,
  count = FALSE
)

Arguments

x

A data frame where the first column contains species (character vector), and the next two columns contain numeric trait values (2D space).

n_bins

Integer. Number of bins per axis (default = 10).

remove.cells

Logical. If `TRUE`, remove empty cells from the PAM (default).

remove.sp

Logical. If `TRUE`, remove species absent from all cells (default).

count

Logical. If `TRUE`, display a text progress bar while building the PAM.

Value

A list with two components:

  • PAM_attribute: a matrix with cell ID, trait coordinates, and species presence (0/1).

  • Attr_Richness_Raster: a raster of richness (number of species) in trait space.

Details

Create a Presence–Absence Matrix in Trait Space

The two trait axes are divided into equal-interval bins, generating a grid of `n_bins × n_bins` cells. Each species occurrence is assigned to a cell, and the resulting PAM indicates which species are present in each trait cell.

Examples

if (FALSE) { # \dontrun{
# n <- 2000
} # }