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ellipsoid_projection: function to project an ellipsoid model

Source: R/ellipsoid_projection.R
ellipsoid_projection.Rd

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

Usage

ellipsoid_projection(
  envlayers,
  centroid,
  covar,
  level = 0.95,
  output = "suitability",
  plot = TRUE,
  size,
  xlab1 = "niche var 1",
  ylab1 = "niche var 2",
  zlab1 = "S",
  alpha = 0.1,
  ...
)

Arguments

envlayers

A SpatRaster 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 ellipsoid (see cov_center).

level

The proportion of points to be included inside the ellipsoid

output

The output distance: two possible values "suitability" or "mahalanobis". By default the function uses "suitability".

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

alpha

Control the transparency of the 3-dimensional ellipsoid

...

Arguments passed to plot3d function from rgl

Value

Returns a SpatRaster of suitability values.

Examples

# \donttest{
library(tenm)
data("abronia")
tempora_layers_dir <- system.file("extdata/bio",package = "tenm")
abt <- tenm::sp_temporal_data(occs = abronia,
                              longitude = "decimalLongitude",
                              latitude = "decimalLatitude",
                              sp_date_var = "year",
                              occ_date_format="y",
                              layers_date_format= "y",
                              layers_by_date_dir = tempora_layers_dir,
                              layers_ext="*.tif$")
abtc <- tenm::clean_dup_by_date(abt,threshold = 10/60)
future::plan("multisession",workers=2)
abex <- tenm::ex_by_date(this_species = abtc,train_prop=0.7)
abbg <- tenm::bg_by_date(this_species = abex,
                         buffer_ngbs=10,n_bg=50000)
future::plan("sequential")
mod <- tenm::cov_center(data = abex$env_data,
                        mve = TRUE,
                        level = 0.975,
                        vars = c("bio_05","bio_06","bio_12"))
layers_path <-   list.files(file.path(tempora_layers_dir,
                                      "2016"),
                            pattern = ".tif$",full.names = TRUE)
elayers <- terra::rast(layers_path)
nmod <- ellipsoid_projection(envlayers = elayers[[names(mod$centroid)]],
                             centroid = mod$centroid,
                             covar = mod$covariance,
                             level = 0.99999,
                             output = "suitability",
                             size = 3,
                             plot = TRUE)
# }