ellipsoidfit: Function fit an ellipsoid model In luismurao/nichetoolbox: From getting biodiversity data to evaluating species distribution models in a friendly GUI environment

Description

Function fit an ellipsoid model using the shape matrix (covariance matrix) of the niche variables.

Usage

 ```1 2 3``` ```ellipsoidfit(data, centroid, covar, level = 0.95, threshold = 0.05, plot = T, size, xlab1 = "niche var 1", ylab1 = "niche var 2", zlab1 = "Suitability", ...) ```

Arguments

 `data` A RasterStack or RasterBrick objet of the niche varibles. `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 `threshold` Threshold value for the suitabilities to be cosidered as 0, by default all suiabilities <0.05 are cosidered as zeros `plot` Logical If True a plot of niche will be shown. `size` The size of the points of the niche plot.

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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14``` ```## Load niche data # d_cardon <- read.csv(system.file("extdata", "cardon_virtual.csv", package = "nichetoolbox")) ## 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 <- stack(list.files(system.file("extdata", # package = "nichetoolbox"), # pattern = ".asc\$",full.names = TRUE)) # Fitting the ellipsoid model # ellipsoidMod <- ellipsoidfit(nicheStack, # covar_centroid\$centroid, # covar_centroid\$covariance, # level=0.95,threshold=0.05,plot=TRUE,size=3) # plot(ellipsoidMod\$suitRaster) ```

luismurao/nichetoolbox documentation built on July 30, 2018, 2:09 p.m.