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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. Should cells with no species be removed from the final matrix?

remove.sp

Logical. Should species with no occurrences in attribute space be removed?

count

Logical. If `TRUE`, displays a progress bar for species processing.

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
Species <- paste0("sp", 1:n)
trait_a <- rnorm(n)
trait_b <- trait_a * .2 + rnorm(n)
x <- data.frame(Species, trait_a, trait_b)
test <- lets.attrpam(x, n_bins = 30)
lets.plot.attrpam(test)
} # }