getDynamicAlphaHull: Generate polygon based on alpha hulls

In rangeBuilder: Occurrence Filtering, Geographic Standardization and Generation of Species Range Polygons

Generate polygon based on alpha hulls

Description

Generates an apha hull polygon, where the alpha parameter is determined by the spatial distribution of the coordinates.

Usage

getDynamicAlphaHull(
  x,
  fraction = 0.95,
  partCount = 3,
  buff = 10000,
  initialAlpha = 3,
  coordHeaders = c("Longitude", "Latitude"),
  clipToCoast = "terrestrial",
  alphaIncrement = 1,
  verbose = FALSE,
  alphaCap = 400
)

Arguments

x	dataframe of coordinates in decimal degrees, with a minimum of 3 rows.
fraction	the minimum fraction of occurrences that must be included in polygon.
partCount	the maximum number of disjunct polygons that are allowed.
buff	buffering distance in meters
initialAlpha	the starting value for alpha
coordHeaders	the column names for the longitude and latitude columns, respectively. If x has two columns, these are assumed to be longitude and latitude, and coordHeaders is ignored.
clipToCoast	Either "no" (no clipping), "terrestrial" (only terrestrial part of range is kept) or "aquatic" (only non-terrestrial part is clipped). See Details.
alphaIncrement	the amount to increase alpha with each iteration
verbose	prints the alpha value to the console, intended for debugging.
alphaCap	Max alpha value before function aborts and returns a minimum convex hull.

Details

From a set of coordinates, this function will create an alpha hull with alpha = initialAlpha, and will then increase alpha by alphaIncrement until both the fraction and partCount conditions are met.

If the conditions cannot be satisfied, then a minimum convex hull is returned.

If clipToCoast is set to "terrestrial" or "aquatic", the resulting polygon is clipped to the coastline, using a basemap from naturalearth. The first time this function is run, this basemap will be downloaded. Subsequent calls will use the downloaded map.

Value

a list with 2 elements:

hull	a sf polygon object
alpha	the alpha value that was found to satisfy the criteria. If a convex hull was returned, this will list MCH.

Author(s)

Pascal Title

See Also

Alpha hulls are created with ahull.

Examples

data(crotalus)

# create a polygon range for Crotalus atrox
x <- crotalus[which(crotalus$genSp == 'Crotalus_atrox'),]
x <- x[sample(1:nrow(x), 50),]

range <- getDynamicAlphaHull(x, coordHeaders=c('decimallongitude','decimallatitude'), 
	clipToCoast = 'no')

plot(range[[1]], col=transparentColor('dark green', 0.5), border = NA)
points(x[,c('decimallongitude','decimallatitude')], cex = 0.5, pch = 3)

# to add a basic coastline, you can use the internal map
# world <- rangeBuilder:::loadWorldMap()
# plot(world, add = TRUE, lwd = 0.5)

rangeBuilder documentation built on March 7, 2023, 5:30 p.m.