extractFromEpmGrid: Extract from epmGrid

In epm: EcoPhyloMapper

Extract from epmGrid

Description

Return species from intersection between spatial points or polygons and a epmGrid object.

Usage

extractFromEpmGrid(x, spatial, returnCells = FALSE, collapse = TRUE)

Arguments

x	object of class epmGrid
spatial	coordinates as either a spatial points object (sp or sf), a matrix/dataframe with two columns, a numeric vector of c(long, lat), or as a spatial polygon object (sp or sf).
returnCells	boolean, if TRUE, cell indices are returned rather than taxa
collapse	boolean; if TRUE, then a vector of unique species is returned, pooled from all cells, if FALSE, then list is returned with species from every cell as intersected by spatial.

Details

If spatial is a spatial object, it will be transformed to the same projection as x if needed. If spatial is not a spatial object, it is assumed to be in the same projection as x.

Value

A vector of species if collapse = TRUE, or a list of species by cell if collapse = FALSE. If returnCells = TRUE, a vector of cell indices that correspond to the rows in the epmGrid sf object.

Author(s)

Pascal Title

Examples

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))

# extract with table of coordinates
extractFromEpmGrid(tamiasEPM, pts)

# extract with spatial points object
extractFromEpmGrid(tamiasEPM, ptsSF)

# extract with spatial polygon
hull <- st_convex_hull(st_union(ptsSF))
extractFromEpmGrid(tamiasEPM, hull)


# returns each cell's contents
extractFromEpmGrid(tamiasEPM, hull, collapse=FALSE)

# collapses results to unique set of species
extractFromEpmGrid(tamiasEPM, hull, collapse=TRUE)

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