polygon_selection: Selection of spatial polygons based on occurrences

In marlonecobos/ellipsenm: Ecological Niche's Characterizations Using Ellipsoids

Selection of spatial polygons based on occurrences

Description

polygon_selection helps in selecting polygons that intersect with occurrences. Buffering polygons, masking raster layers, and writing results can also be performed if needed.

Usage

polygon_selection(data, longitude, latitude, polygons,
                  buffer_distance = NULL, raster_layers = NULL,
                  clip = FALSE, dissolve = FALSE, mask = FALSE,
                  save = FALSE, name = "calib_area_poligons")

Arguments

data	data.frame of occurrence records containing at least longitude and latitude columns.
longitude	(character) name of the column with longitude data.
latitude	(character) name of the column with latitude data.
polygons	SpatialPolygon* object.
buffer_distance	(numeric) distance in km to be used to create a buffer for the concave hull. Default = NULL.
raster_layers	optional RasterStack to be used in restricting the resulting SpatialPolygon and in preparing variables for further processing. Default = NULL.
clip	(logical) whether or not to clip polygons considering boundaries of layers in raster_layers. Using this option increases the time of processing considerably. Default = FALSE.
dissolve	(logical) whether or not to dissolve polygons. Default = FALSE.
mask	(logical) whether or not to mask the raster_layers to the area created with thsi function. Default = FALSE.
save	(logical) whether or not to write the results in the working directory. Default = FALSE.
name	(character) name of a folder to be written with the results if save = TRUE. Default = "calib_area_concave".

Value

If raster layers are masked, a lits containing a SpatialPolygonDataFrame and a RasterStack of the masked layers.

If raster layers are not masked, a SpatialPolygonDataFrame.

If save = TRUE, results are written in a folder named as in name.

Examples

# reading data
occurrences <- read.csv(system.file("extdata", "occurrences.csv",
                                    package = "ellipsenm"))

spatial_poly <- #HERE YOUR SPATIAL POLYGON OBJECT

# selecting polygons
sp_area <- polygon_selection(data = occurrences, longitude = "longitude",
                             latitude = "latitude", polygons = spatial_poly)

sp::plot(sp_area)
points(occurrences[, 2:3])

# selecting polygons with buffers
sp_area1 <- polygon_selection(data = occurrences, longitude = "longitude",
                              latitude = "latitude", polygons = spatial_poly,
                              buffer_distance = 50)

sp::plot(sp_area1)
points(occurrences[, 2:3])

# selecting polygons, masking layers
vars <- raster::stack(list.files(system.file("extdata", package = "ellipsenm"),
                                 pattern = "bio", full.names = TRUE))

sp_area3 <- polygon_selection(data = occurrences, longitude = "longitude",
                              latitude = "latitude", polygons = spatial_poly,
                              buffer_distance = 50, raster_layers = vars,
                              mask = TRUE)

raster::plot(sp_area3$masked_variables[[1]])
sp::plot(sp_area3$calibration_area, add = TRUE)
points(occurrences[, 2:3])

# selecting polygons, masking layers, and saving results
sp_area4 <- polygon_selection(data = occurrences, longitude = "longitude",
                              latitude = "latitude", polygons = spatial_poly,
                              buffer_distance = 50, raster_layers = vars,
                              mask = TRUE, save = TRUE, name = "p_selection")

# check directory
dir()

marlonecobos/ellipsenm documentation built on Oct. 18, 2023, 8:09 a.m.