Plot a nicheR ellipsoid in 3D environmental space — plot_ellipsoid

Creates an interactive 3D plot of a nicheR_ellipsoid object with support for background points or suitability surfaces.

Usage

plot_ellipsoid_3d(object, dim = c(1, 2, 3), wire = FALSE, aspect = TRUE,
                  background = NULL, prediction = NULL, col_layer = NULL,
                  pal = hcl.colors(100, palette = "Viridis"),
                  rev_pal = FALSE, bg_sample = NULL, col_ell = "#8b0000",
                  alpha_ell = 1, alpha_bg = 1, col_bg = "#8A8A8A",
                  fixed_lims = NULL, xlab = NULL, ylab = NULL,
                  zlab = NULL, ...)

Arguments

object: A nicheR_ellipsoid object constructed with at least 3 dimensions.
dim: Integer vector of length 3. Indices of dimensions to plot.
wire: Logical. If TRUE, plots wireframe. The default, FALSE, plots a shaded volume.
aspect: Logical. If TRUE, maintains aspect ratio (1:1:1).
background: Optional data frame/matrix of background points. This argument has priority over prediction if both are provided.
prediction: Optional data frame/matrix for prediction surfaces.
col_layer: Character or NULL. Column in prediction to use for coloring.
pal: Color palette function or character vector.
rev_pal: Logical. If TRUE, reverses the palette.
bg_sample: Integer or NULL. Subsample size for large data.
col_ell: Color of the ellipsoid. Default is "#000000".
alpha_ell: Transparency of the ellipsoid. Default is 1. Not applied to wireframe mode.
alpha_bg: Transparency of background points. Default is 1. Also applied to prediction points.
col_bg: Color for background points.
fixed_lims: Named list with xlim, ylim, and zlim.
xlab: x-axis label. The default, NULL, uses ellipsoid object variable names, if any found.
ylab: y-axis label. The default, NULL, uses ellipsoid object variable names, if any found.
zlab: z-axis label. The default, NULL, uses ellipsoid object variable names, if any found.
...: Additional graphical parameters.

Value

A 3d plot of the ellipsoid in E-space, shown in viewer.

Examples

# Building an ellipsoid
## Define ranges for three variables
range <- data.frame(bio_1  = c(22, 32),
                    bio_12 = c(800, 4200),
                    bio_15 = c(45, 115))

## Build the ellipsoid
ell5 <- build_ellipsoid(range = range)
#> Starting: building ellipsoidal niche from ranges...
#> Step: computing covariance matrix...
#> Step: computing additional ellipsoidal niche metrics...
#> Done: created ellipsoidal niche.
ell5$cov_limits
#>                        min     max
#> bio_1-bio_12   -472.222222  935.00
#> bio_1-bio_15     -9.722222   19.25
#> bio_12-bio_15 -3305.555555 6545.00

ell5 <- update_ellipsoid_covariance(ell5, c("bio_1-bio_12" = 200,
                                            "bio_1-bio_15" = 0,
                                            "bio_12-bio_15" = -3000))
#> Starting: updating covariance values...
#> Step: computing ellipsoid metrics...
#> Done: updated ellipsoidal niche metrics

# Plot the ellipsoid in 3D
# \donttest{
if(requireNamespace("rgl", quietly = TRUE)){
  plot_ellipsoid_3d(ell5)
 }
3D plot

# }