Example niche ellipsoid objects for virtual communities

Pre-calculated nicheR_ellipsoid objects representing hypothetical species niches based on bioclimatic variables. These objects are primarily used in the package vignettes and examples to demonstrate ellipsoid creation, covariance adjustments, visual comparisons, and multidimensional niches.

Usage

example_sp_1

example_sp_2

example_sp_3

example_sp_4

Format

Objects of class nicheR_ellipsoid (which are lists) with 13 elements:

dimensions: Integer. Number of dimensions (2 or 3).
var_names: Character vector. Names of variables (e.g., "bio_1", "bio_12").
centroid: Named numeric vector. The center of the niche (\(\mu\)).
cov_matrix: Matrix. The covariance matrix (\(\Sigma\)).
Sigma_inv: Matrix. The precision matrix (inverse covariance).
chol_Sigma: Matrix. Cholesky decomposition of the covariance.
eigen: List. Eigenvectors and eigenvalues of the covariance.
cl: Numeric. Confidence level used (e.g., 0.99).
chi2_cutoff: Numeric. The chi-square quantile for the given cl.
semi_axes_lengths: Numeric vector. Radii of the ellipsoid axes.
axes_coordinates: List. Vertices (endpoints) for each ellipsoid axis.
volume: Numeric. The hyper-volume of the ellipsoid.
cov_limits: List. Axis-aligned minimum and maximum covariance limits.

An object of class nicheR_ellipsoid of length 13.

An object of class nicheR_ellipsoid of length 14.

Details

These objects serve as templates for testing community simulation and projection functions. They were generated using build_ellipsoid and modified with update_ellipsoid_covariance to reflect distinct ecological strategies:

example_sp_1: A 2D niche (bio_1, bio_12) with a broad, warm-climate preference and wide precipitation tolerance. It includes a positive covariance (750) between temperature and precipitation.
example_sp_2: A 2D niche (bio_1, bio_12) shifted toward cooler and wetter environments compared to example_sp_1, with a positive covariance (500).
example_sp_3: A 2D niche (bio_1, bio_12) representing a warm-adapted specialist restricted to dry environments. It has a much smaller niche volume and a slight positive covariance (120).
example_sp_4: A 3D niche (bio_1, bio_12, bio_15) adapted to seasonally pulsed precipitation environments. It features a strong negative covariance (-5000) between annual precipitation and precipitation seasonality.

Examples

data(example_sp_1)
print(example_sp_1)
#> nicheR Ellipsoid Object
#> -----------------------
#> Dimensions:        2D
#> Chi-square cutoff: 9.21
#> Centroid (mu):     26, 2375
#> 
#> Covariance matrix:
#>        bio_1   bio_12
#> bio_1      4    750.0
#> bio_12   750 293402.8
#> 
#> Covariance Limits:
#>                    min      max
#> bio_1-bio_12 -1083.333 1083.333
#> 
#> Ellipsoid semi-axis lengths:
#>   1643.885, 4.38
#> 
#> Ellipsoid axis endpoints:
#>  Axis 1:
#>           bio_1   bio_12
#> vertex_a 21.798  731.121
#> vertex_b 30.202 4018.879
#> 
#>  Axis 2:
#>          bio_1   bio_12
#> vertex_a 30.38 2374.989
#> vertex_b 21.62 2375.011
#> 
#> Ellipsoid volume:  22619.64
#> 

# Access the volume of the 2D broad warm-climate niche
example_sp_1$volume
#> [1] 22619.64

# Access the covariance matrix of the 3D seasonal precipitation niche
data(example_sp_4)
example_sp_4$cov_matrix
#>             bio_1   bio_12     bio_15
#> bio_1    2.777778    200.0     0.0000
#> bio_12 200.000000 321111.1 -5000.0000
#> bio_15   0.000000  -5000.0   136.1111

Example niche ellipsoid objects for virtual communities

Usage

Format

Details

See also

Examples