sdm_extract: Extract environmental data values from a spatial raster based...

In sjevelazco/flexsdm: Tools for Data Preparation, Fitting, Prediction, Evaluation, and Post-Processing of Species Distribution Models

Extract environmental data values from a spatial raster based on x and y coordinates

Description

Extract environmental data values from a spatial raster based on x and y coordinates

Usage

sdm_extract(data, x, y, env_layer, variables = NULL, filter_na = TRUE)

Arguments

data	data.frame. Database with species presence, presence-absence, or pseudo-absence records with x and y coordinates
x	character. Column name with spatial x coordinates
y	character. Column name with spatial y coordinates
env_layer	SpatRaster. Raster or raster stack with environmental variables.
variables	character. Vector with the variable names of predictor (environmental) variables Usage variables. = c("aet", "cwd", "tmin"). If no variable is specified, function will return data for all layers. Default NULL
filter_na	logical. If filter_na = TRUE (default), the rows with NA values for any of the environmental variables are removed from the returned tibble.

Value

A tibble that returns the original data base with additional columns for the extracted environmental variables at each xy location from the SpatRaster object used in 'env_layer'

Examples

## Not run: 
require(terra)

# Load datasets
data(spp)
f <- system.file("external/somevar.tif", package = "flexsdm")
somevar <- terra::rast(f)

# Extract environmental data from somevar for all locations in spp
ex_spp <-
  sdm_extract(
    data = spp,
    x = "x",
    y = "y",
    env_layer = somevar,
    variables = NULL,
    filter_na = FALSE
  )

# Extract environmental for two variables and remove rows with NAs
ex_spp2 <-
  sdm_extract(
    data = spp,
    x = "x",
    y = "y",
    env_layer = somevar,
    variables = c("CFP_3", "CFP_4"),
    filter_na = TRUE
  )

ex_spp
ex_spp2

## End(Not run)

sjevelazco/flexsdm documentation built on Feb. 28, 2025, 9:07 a.m.