cov_center: Function to compute the Minimum Volume covariance Matrix of...

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

Function to compute the Minimum Volume covariance Matrix of an ellipsoid niche model.

Description

Function to compute the covariance matrix, the niche centroid, and volume of an ellipsoid model. ellipsoid model. It uses the values of the niche variables of the occurrence points.

Usage

cov_center(data, mve = TRUE, level, vars = NULL)

Arguments

data	A data.frame or a matrix with the numeric values of the variables that will be used to model the niche.
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.
level	A numerical value specifying the proportion of the data to be used to compute the ellipsoid.
vars	A numeric or a string vector specifying the columns indexes/names of the variables of the input data which will be used to fit the ellipsoid model. If NULL the user will be asked to enter the indexes. interactively

Value

Returns a list containing the centroid of the ellipsoid, the covariance matrix based on the input data, ellipsoid volume, semi-axis length, and axis coordinates.

Examples

environ_data <- read.csv(system.file("extdata",
                                     "nichekmeansCluster.csv",
                                      package = "ntbox"))[,-(1:3)]
ellipsoid_metadata <- cov_center(environ_data,mve = TRUE,
                                 level=0.975,
                                 vars = c("bio5","bio6","bio12"))
# Ellipsoid center
ellipsoid_metadata$centroid
# Shape matrix
ellipsoid_metadata$covariance
# Ellipsoid volume
ellipsoid_metadata$niche_volume
## Not run: 
# Plot ellipsoid
rgl::plot3d(rgl::ellipse3d(ellipsoid_metadata$covariance,
                           centre = ellipsoid_metadata$centroid,
                           level = 0.99999),
            alpha=0.4,col="blue")
rgl::points3d(environ_data[,c("bio5","bio6","bio12")])

## End(Not run)

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