ellipsoidfit2: ellipsoidfit2: function to fit an ellipsoid model

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

ellipsoidfit2: function to fit an ellipsoid model

Description

Function to fit an ellipsoid model using the shape matrix (covariance matrix) of the niche variables. This is an optimized version of the ellipsoidfit function; the diffrence is that it does not give the table of distances to niche centroid.

Usage

ellipsoidfit2(
  envlayers,
  centroid,
  covar,
  level = 0.95,
  plot = T,
  size,
  xlab1 = "niche var 1",
  ylab1 = "niche var 2",
  zlab1 = "S",
  ...
)

Arguments

envlayers	A RasterStack or RasterBrick object of the niche variables.
centroid	A vector with the values of the centers of the ellipsoid (see cov_center).
covar	The shape matrix (covariance) of the ellipoid (see cov_center).
level	The proportion of points to be included inside the ellipsoid
plot	Logical If True a plot of the niche will be shown.
size	The size of the points of the niche plot.
xlab1	For x label for 2-dimensional histogram
ylab1	For y label for 2-dimensional histogram
zlab1	For z label for 2-dimensional histogram
...	Arguments passed to plot3d function from rgl

Value

Returns a list containing a data.frame with the suitability values; a suitability raster; a data.frame with the mahalanobis and euclidean distances to the centroid.

Examples

## Load niche data
## Not run: 
d_cardon <-  read.csv(system.file("extdata", "cardon_virtual.csv", package = "ntbox"))
## Compute the centroid and shape (covariance matrix) of the ellipsoid model.
covar_centroid <- cov_center(d_cardon,mve=TRUE,level=0.99,vars=c(3,4,5))
## RasterStack with the niche variables
nicheStack <- raster::stack(list.files(system.file("extdata",
                                       package = "ntbox"),
                                       pattern = ".asc$",
                                       full.names = TRUE))
# Fitting the ellipsoid model
 ellipsoidMod <- ellipsoidfit2(envlayers = nicheStack,
                               centroid = covar_centroid$centroid,
                               covar = covar_centroid$covariance,
                               level=0.99,
                               plot=TRUE,
                               size=3)
 raster::plot(ellipsoidMod)

## End(Not run)

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