YplantQMC (version 0.6-3)

STARbar: Calculate displayed and projected leaf areas of a 3D plant

Description

From a 3D plant, calculates the area of all leaves facing the viewing angle (from a given azimuth and altitude), or 'projected area', and the area of the leaves that is visible ('displayed area'). By default, repeats calculations from many viewing angles to estimate the hemi-spherically averaged STAR. This function calculates the displayed area (DA) and projected area (PA) of the entire plant, either over some specified viewing angle(s), or (by default) the hemispherically average values. From these averages, the average STAR is estimated (see Duursma et al. 2012). The summary.plant3d function also calculates STARbar, if calcSTARbar=TRUE is set. There are four methods for the calculation of the displayed and projected area from a given viewing angle: [object Object],[object Object],[object Object],[object Object] There are three integration methods. Note that if method = "QuasiMC", the integration method is ignored. [object Object],[object Object],[object Object]

Usage

STARbar(object, ...)

## S3 method for class 'plant3dlist':
STARbar(object, quiet = FALSE, ...)

## S3 method for class 'plant3d':
STARbar(object, method = c("gridtracer", "exact", "QuasiMC",
  "slowquasimc"), integration = c("Turtlesky", "Yplant", "Turtle244"),
  progressbar = TRUE, returnldr = FALSE, quiet = FALSE, npside = 25,
  silhouette = TRUE, azimuth = NA, altitude = NA, ...)

Arguments

object

An object of class 'plant3d', see constructplant

quiet

If TRUE, prints no progress to the screen.

method

The method to calculate the displayed area. See Details.

integration

The integration method to calculate the average STAR over the hemisphere. See Details.

progressbar

If TRUE (default), displays a graphical progress bar.

returnldr

If TRUE, returns a dataframe with results per viewing angle.

npside

For method = "gridtracer", the number of grid cells per side for raytracing.

silhouette

If TRUE, also calculates the 2D convex hull around the projected plant (see Silhouette).

azimuth,altitude

Azimuth and altitude of the viewing direction (Optional, in Radians).

...

Further arguments are ignored, for now.

References

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. See also http://www.remkoduursma/yplantqmc

See Also

projectplant,constructplant,Silhouette, summary.plant3d

Examples

# Get STARbar for the built-in Toona plant:
# (Settings are fast, not accurate)
STARbar(toona, method="gridtracer", npside=15)

# For exact STAR, use:
STARbar(toona, method="exact")

# To produce an LDR file (as in the original Yplant), use:
clidstar <- STARbar(toona, method="gridtracer", npside=30, integration="Yplant", returnldr=T)
write.table(clidstar$ldr, "toona.LDR")