rangeBuilder (version 2.1)

getDynamicAlphaHull: 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
)

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.

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.

Author

Pascal Title

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.

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)