define_accessibleArea: Generate accessible area for a species distribution model to...

In mbelitz/autoSDM: What the Package Does (One Line, Title Case)

Description

Determine accessible area for a SDM to be projected to in geographic space. This is done using either an alpha or convex hull approach, where the buffer to the hull is either 1) a user defined distance in meters, 2) a percentile distance between points, or 3) the maximum distance of either the user defined distance or the percentile distance between points.

Usage

define_accessibleArea(
  df,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  species = "scientificName",
  shape = "alpha",
  minBuffDist,
  quantile = 0.8,
  dis_type = "max",
  clipCoast = "terrestrial"
)

Arguments

df	a data.frame containing the coordinates (e.g., latitude and longitude) of a the occurrence records.
lon	a character string containing the column name with the longitudinal coordinates. Default = "decimalLongitude".
lat	a character string containing the column name with the latitudinal coordinates. Default = "decimalLatitude".
species	a character string containing the binomial of the species whose distribution is being modeled. Default = "scientificName".
shape	a character string of either "alpha" or "convex" determining if the polygon around the occurrence records should be an alpha or convex hull. Default = "alpha".
quantile	a double value between the range of 0 and 1 that represents the a quantile distance between points (e.g., the 0.8th quantile distance between occurrence records). Default = 0.8
dis_type	character string of either "meters", "Q", or "max" denoting if the buffered distance should be a user defined value in meters ("meters"), a quantile determined distance between points ("Q), or the maximum value between the other two options ("max"). Default = "max".
clipCoast	Either "no" (no clipping), "terrestrial" to only keep terrestrial part of range or "aquatic" to only keep non-terrestrial part of range. Default = "terrestrial".
minBuff	a numeric value denoting the buffer in meters for the polygon around the occurrence points.

Value

a spatial polygon representing the accessible area for a species' distribution.

Examples

# generate test data.frame
test_data <- data.frame(species = "Test species",
decimallongitude = runif(100, min = 42, max = 51),
decimallatitude = runif(100, min = -26, max = -11))

# flag potentially problematic coordinates using CoordinateCleaner Function
# only keep non-flagged coordinates
cc <- dplyr::filter(CoordinateCleaner::clean_coordinates(x = test_data),
.summary == TRUE)

aa <- define_accessibleArea(df = cc,
lon = "decimallongitude", lat = "decimallatitude",
minBuffDist = 100000)
plot(aa)

mbelitz/autoSDM documentation built on Dec. 21, 2021, 3:55 p.m.