generateOccurrenceMatrix: Convert epmGrid to community matrix

In epm: EcoPhyloMapper

Convert epmGrid to community matrix

Description

Given specific sites (or all sites), convert epmGrid to a species occurrence matrix, with sites as rows, and species as columns.

Usage

generateOccurrenceMatrix(x, sites)

Arguments

x	object of class epmGrid
sites	locations of sites, see details.

Details

If sites are site coordinates, then this should be a dataframe or matrix with two columns; if sites are cell indices, then a numeric vector; if sites = 'all', then all cells will be returned as sites.

To get the associated site coordinates, see coordsFromEpmGrid.

Value

a presence/absence matrix, with sites as rows and species as columns.

Author(s)

Pascal Title

Examples

tamiasEPM

# from cell indices
cells <- c(2703, 90, 3112, 179)
generateOccurrenceMatrix(tamiasEPM, cells)

# get the associated site coordinates
coordsFromEpmGrid(tamiasEPM, cells)

# from coordinates
library(sf)
# get the projection of the epmGrid object
proj <- summary(tamiasEPM)$crs
# define some points
pts <- rbind.data.frame(
		c(-120.5, 38.82),
		c(-84.02, 42.75),
		c(-117.95, 55.53))
colnames(pts) <- c('x', 'y')
ptsSF <- st_as_sf(pts, coords = 1:2, crs = "epsg:4326")
pts <- st_coordinates(st_transform(ptsSF, crs = proj))

generateOccurrenceMatrix(tamiasEPM, pts)

epm documentation built on April 4, 2025, 1:42 a.m.