pavo (version 2.9.0)

vol: Plot a tetrahedral colour space

Description

Produces a 3D colour volume in tetrahedral colour space when plotting a non-interactive tetrahedral plot.

Usage

vol(
  tcsdata,
  type = c("convex", "alpha"),
  avalue = "auto",
  alpha = 0.2,
  grid = TRUE,
  fill = TRUE,
  new = FALSE,
  ...
)

Value

vol() creates a 3D colour volume within a static tetrahedral plot.

Arguments

tcsdata

(required) a data frame, possibly a result from the colspace() or tcspace() function, containing values for the 'x', 'y' and 'z' coordinates as columns (labeled as such).

type

if "convex", the colour volume is plotted using a convex hull and if "alpha", it is plotted using alphashapes.

avalue

if type = "alpha", which alpha parameter value should be used to compute the alphashape. avalue = "auto" (default) finds and use the \(\alpha^*\) value as defined in Gruson (2020).

alpha

transparency of volume (if fill = TRUE).

grid

logical. if TRUE (default), draws the polygon outline defined by the points.

fill

logical. if TRUE (default), fills the volume defined by the points.

new

logical. Should a new plot be started or draw over an open plot? (defaults to FALSE)

...

additional graphical options. See polygon() and tetraplot().

Author

Rafael Maia

Hugo Gruson

References

Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.

Stoddard, M. C., & Stevens, M. (2011). Avian vision and the evolution of egg color mimicry in the common cuckoo. Evolution, 65(7), 2004-2013.

Maia, R., White, T. E., (2018) Comparing colors using visual models. Behavioral Ecology, ary017 tools:::Rd_expr_doi("10.1093/beheco/ary017")

Gruson H. (2020). Estimation of colour volumes as concave hypervolumes using \(\alpha\)-shapes. Methods in Ecology and Evolution, 11(8), 955-963 tools:::Rd_expr_doi("10.1111/2041-210X.13398")

Examples

# For plotting
data(sicalis)
vis.sicalis <- vismodel(sicalis, visual = "avg.uv")
tcs.sicalis <- colspace(vis.sicalis, space = "tcs")
plot(tcs.sicalis)

# Convex hull
vol(tcs.sicalis, type = "convex")

# Alpha-shape
if (require("alphashape3d")) {
  vol(tcs.sicalis, type = "alpha", avalue = 1)
}