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

In luismurao/hsi: "Habitat suitability index"

Description

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

## Not run: 
cardon_data <- read.csv(system.file("exdata/cardon_virtual.csv",
                                    package = "hsi"))
cardon_ellipsoid <- cov_center(data=cardon_data, mve=TRUE, level=0.975,
                               vars=c("bio5","bio6", "bio12"))
# To obtain the coordinates of the ellipsoid's centroid run:
print(cardon_ellipsoid$centroid)

# To obtain the coordinates of the ellipsoid's minimum value covariance run:
print(cardon_ellipsoid$covariance)

# To obtain the coordinates of the ellipsoid's niche volume run:
print(cardon_ellipsoid$niche_volume)

# To obtain the coordinates of the ellipsoid's Semi Axis Length run:
print(cardon_ellipsoid$SemiAxis_length)

# To obtain the coordinates of the ellipsoid's coordinates run:
print(cardon_ellipsoid$axis_coordinates)

# To plot the ellipsoid with a 99% of data conteined from the obtained
# by minimim volume method
library(rgl)
ellipsoid_coor <- rgl::ellipse3d(x=cardon_ellipsoid$covariance,centre=cardon_ellipsoid$centroid,
                                 level=0.99)

rgl::plot3d(ellipsoid_coor, alpha=0.3)


## End(Not run)

luismurao/hsi documentation built on Dec. 26, 2021, 9:53 a.m.