Function to plot clusters in 3-dimensions. — ellipsoid_cluster_plot

Plot cluster data in 3D by modeling them as an Ellipsoid.

ellipsoid_cluster_plot_3d(
  niche_data,
  cluster_ids,
  x,
  y,
  z,
  mve = FALSE,
  ellips = TRUE,
  level = 0.975,
  alpha,
  grupos,
  vgrupo,
  cex1 = 0.25
)

Arguments

niche_data	A data.frame or matrix containing niche variables
cluster_ids	Cluster ids
x	variable on x-axes
y	variable on y-axes
z	variable on z-axes
mve	A logical value. If TRUE a minimum volume ellipsoid will be computed using the function `cov.rob` of the MASS package. If False the covariance matrix of the input data will be used.
ellips	Ellipsoid plot of each cluster
level	proportion of points inside the ellipsoid.
alpha	Transparency level of ellipsoid plots
grupos	Logical. Show ids of a geographic grouping variable
vgrupo	A vector containing the levels of the geographic grouping variable
cex1	Point size

Value

Returns a list of the ellipsoid metadata for each cluster.

Details

The output of this function is the same of the cov_center function.

Examples

if (FALSE) {
cluster_data <- read.csv(system.file("extdata",
                                     "nichekmeansCluster.csv",
                                      package = "ntbox"))

ellipsoid_clusters <- ellipsoid_cluster_plot_3d(niche_data =environ_data[,c("bio5","bio6","bio12")],
                                                cluster_ids = cluster_data$cluster,
                                                x = "bio5",y="bio6",z="bio12",mve = T,
                                                ellips = T,alpha = 0.25,
                                                grupos = T,vgrupo =cluster_data$cluster,
                                                cex1 = 1,level = 0.975)
# Print metadata for the Minimum Volume Ellipsoid that belongs to cluster 1
print(ellipsoid_clusters$cluster_n_1)
}