set_calibarea_b: Create minimum convex polygon based on coordinates of species...

In HemingNM/ENMwizard: Advanced Techniques for Ecological Niche Modeling Made Easy

Create minimum convex polygon based on coordinates of species occurence data for several species

Description

This function will use a list of coordinates of species occurence data and create minimum convex polygons for each element in the list. It is possible to create concave or convex polygons, create several small polygons based on clusters of points.

Usage

set_calibarea_b(
  spp.occ.list,
  k = 1,
  c.m = "AP",
  r = 2,
  q = 0.3,
  distance = "euclidean",
  min.nc = 2,
  max.nc = 20,
  method = "mcquitty",
  index = "all",
  alphaBeale = 0.1,
  convex = T,
  alpha = 10,
  plot = F,
  save = T,
  save.pts = F,
  numCores = 1,
  crs.set = "+proj=longlat +datum=WGS84"
)

Arguments

spp.occ.list	A named list of species occurence points, either as "data.frame" or "SpatialPoints"/"SpatialPointsDataFrame"
k	number of polygons to create based on coordinates
c.m	clustering method to find the best number of clusters (k). Currently E (Elbow) or (Affinity Propagation).
r	exponent (see details below)
q	if p=NA, exemplar preferences are initialized according to the distribution of non-Inf values in s. If q=NA, exemplar preferences are set to the median of non-Inf values in s. If q is a value between 0 and 1, the sample quantile with threshold q is used, whereas q=0.5 again results in the median.
distance	the distance measure to be used to compute the dissimilarity matrix. This must be one of: "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski" or "NULL". By default, distance="euclidean". If the distance is "NULL", the dissimilarity matrix (diss) should be given by the user. If distance is not "NULL", the dissimilarity matrix should be "NULL".
min.nc	minimal number of clusters, between 1 and (number of objects - 1)
max.nc	maximal number of clusters, between 2 and (number of objects - 1), greater or equal to min.nc. By default, max.nc=15.
method	type of distance measure to be used; for negDistMat, expSimMat and linSimMat, this argument is analogous to the method argument of dist. For corSimMat, this argument is analogous to the method argument of cor.
index	the index to be calculated. This should be one of : "kl", "ch", "hartigan", "ccc", "scott", "marriot", "trcovw", "tracew", "friedman", "rubin", "cindex", "db", "silhouette", "duda", "pseudot2", "beale", "ratkowsky", "ball", "ptbiserial", "gap", "frey", "mcclain", "gamma", "gplus", "tau", "dunn", "hubert", "sdindex", "dindex", "sdbw", "all" (all indices except GAP, Gamma, Gplus and Tau), "alllong" (all indices with Gap, Gamma, Gplus and Tau included).
alphaBeale	significance value for Beale's index.
convex	Logical. Convex (T) or concave (F) polygon
alpha	Value of \alpha.
plot	logical. Plot results or not?
save	Should save polygons on disk?
save.pts	logical. Save each species' occurence points as shapefile?
numCores	Number of cores to use for parallelization. If set to 1, no paralellization is performed
crs.set	set the coordinate reference system (CRS) of the polygons

See Also

set_calibarea, split_poly, NbClust #' @return A named list of spatial polygons built using coordinates

Examples

## Not run: 
Bvarieg.occ <- read.table(paste(system.file(package="dismo"),
 "/ex/bradypus.csv", sep=""), header=TRUE, sep=",")
colnames(Bvarieg.occ) <- c("SPEC", "LONG", "LAT")
spp.occ.list <- list(Bvarieg = Bvarieg.occ)
occ.polys <- set_calibarea_b(spp.occ.list)
occ.polys <- set_calibarea_b(spp.occ.list, convex=TRUE, alpha=10)

## End(Not run)

HemingNM/ENMwizard documentation built on Jan. 4, 2024, 3:24 p.m.