cov_center: Function to compute the shape (covarince) and center of an...

In luismurao/nichetoolbox: From getting biodiversity data to evaluating species distribution models in a friendly GUI environment

Description

Function to compute covariance and the center of an ellipsoid model using 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 vector specifying the columns indexes 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 and the input data.

Examples

## Load niche data
# d_cardon <-  read.csv(system.file("extdata", "cardon_virtual.csv", package = "nichetoolbox"))
## Look the data
# head(d_cardon)
## Compute the centroid and shape (covariance matrix) of the ellipsoid model.
## The user will be asked to enter the variables indexes
#covar_centroid <- cov_center(d_cardon,mve=TRUE,level=0.99,vars=NULL)
## Alternatively you can specify the columns indexes of the variables
# covar_centroid <- cov_center(d_cardon,mve=TRUE,level=0.99,vars=c(3,4,5))

#+++++++++++++++++++++++++++++ Check the output +++++++++++++++++++++++++++++#
## ellipsoid center
# covar_centroid$centroid
## ellipsoid shape
# covar_centroid$covariance
## Data input
# head(covar_centroid$data)

luismurao/nichetoolbox documentation built on May 21, 2019, 8:56 a.m.