YplantQMC (version 0.6-6)

crownhull: Calculates and plots the convex hull around the plant crown

Description

This function finds the convex hull (and its surface area and volume) spanning the leaves of the 3D plant, using all coordinates of the leaf edges. The result is smallest set of x, y, z points that defines the convex hull, that is, the polyhedral surface that contains all other points, and is convex.

The implementation is a wrapper for the 'convhulln' function in the from package 'geometry'.

Optionaly, uses the 'rgl' package (see plot3d), to add a plot of the hull to the current (rgl) device. Opens a new device if none is currently open. Uses the non-visible function triangles3d to plot the hull, see details there.

The convex hull is calculated with the qhull algorithm, see convhulln and references therein.

Usage

crownhull(xyz, plotit = TRUE, alpha = 0.8)

Arguments

xyz

An object of class 'plant3d', or a matrix with three columns (xyz coordinates).

plotit

Logical. If FALSE, returns only volume and surface area.

alpha

Transparency (0-1).

Value

A list with components 'crownvolume' and 'crownsurface', giving the volume and surface of the convex hull.

References

www.qhull.org,

Duursma, R.A., D.S. Falster, F. Valladares, F.J. Sterck, R.W. Pearcy, C.H. Lusk, K.M. Sendall, M. Nordenstahl, N.C. Houter, B.J. Atwell, N. Kelly, J.W.G. Kelly, M. Liberloo, D.T. Tissue, B.E. Medlyn and D.S. Ellsworth. 2012. Light interception efficiency explained by two simple variables: a test using a diversity of small- to medium-sized woody plants. New Phytologist. 193:397-408.

Examples

# Toona example (plant included in package).
crownhull(toona)


# Some xyz data:
coords <- matrix(runif(300,0,1),ncol=3)
library(rgl)
plot3d(coords, col="blue", size=3, axes=FALSE, box=FALSE, xlab="", ylab="", zlab="")
crownhull(coords)