ellipsoid_cluster_plot_3d: Function to plot clusters in 3-dimensions.

In luismurao/ntbox: From Getting Biodiversity Data to Evaluating Species Distribution Models in a Friendly GUI Environment

Function to plot clusters in 3-dimensions.

Description

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

Usage

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

Details

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

Value

Returns a list of the ellipsoid metadata for each cluster.

Examples

## Not run: 
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)

## End(Not run)

luismurao/ntbox documentation built on Nov. 22, 2024, 4 a.m.