split_poly: Split a species occ polygon (whenever distribution seems...

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

Split a species occ polygon (whenever distribution seems disjoint) into K polygons and save in a single .shp

Description

Cluster points and create several small polygons. Implemented methods are 'Hierarchical Clustering' (when 'k' number of clusters is defined 'k > 0'), 'Elbow' (c.m = "E"), 'Affinity Propagation' (c.m = AP), and several methods implemented in function NbClust of NbClust package (c.m = "NB"). To use NbClust package, check arguments 'distance', 'min.nc', 'max.nc', 'method', and 'index' in ?NbClust::NbClust.

Usage

split_poly(
  occ.spdf,
  k = NULL,
  nm.col.dt = NULL,
  c.m = "NB",
  r = 2,
  q = 0.3,
  distance = "euclidean",
  min.nc = 1,
  max.nc = 20,
  method = "centroid",
  index = "trcovw",
  alphaBeale = 0.1,
  convex = TRUE,
  alpha = 10,
  sp.nm = "species",
  save = T,
  crs.set = "+proj=longlat +datum=WGS84"
)

Arguments

occ.spdf	An object of class SpatialPoints or SpatialPointsDataFrame (e.g. species occurence coordinates)
k	number of polygons to create based on coordinates
nm.col.dt	"character". Name of a numeric column to use as grouping variable in addition to 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.
sp.nm	Species name, used on saving shapefile
save	Should save polygons on disk?
crs.set	set the coordinate reference system (CRS) of the polygons

Value

spatial polygons built using coordinates

See Also

set_calibarea, set_calibarea_b, NbClust

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$Bvarieg <- split_poly(occ.spdf = spp.occ.list$Bvarieg, k=5)

## End(Not run)

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