Last data update: 2014.03.03

R: Fits a leaf angle distribution
fitdistributionR Documentation

Fits a leaf angle distribution

Description

Fits one of nine leaf angle distributions to data, using either log-likelihood (the preferred method), or a method based on minimizing the chi-squared statistic. This latter method is included to be consistent with Wang et al. (2007), as well as others.

A leaf angle distribution is a distribution valid for 0 <= x <= 90.

Usage

fitdistribution(angles, distribution, fitmethod = c("loglik", "chisq"), 
  ellipsmethod = 2, degrees = TRUE, ...)

Arguments

angles

Vector of leaf angles (0-90 degrees, or 0 - pi/2 radians)

distribution

Name of the distribution. Currently included are 'ellipsoid', 'rotatedell', 'twoparbeta', 'spherical', 'planophile', 'extremophile', 'erectophile', 'uniform', and 'plagiophile'.

fitmethod

Method to fit the distribution, either "loglik" (log-likelihood) or "chisq" (chi-squared statistic).

ellipsmethod

If distribution='ellipsoid', and ellipsmethod=1, the method reported by Wang et al. 2007 is used. Not recommended.

degrees

If TRUE, the default, the sample of angles is in degrees, otherwise radians.

...

Other parameters passed to ftheta.

Details

See drawsample to simulate from a fitted leaf angle distribution, and fitalldistributions for a convenience function to fit all built-in distributions to one dataset.

Value

Returns an object of class 'angledist'. Methods exist for print, summary, and plot. See Examples.

Author(s)

Remko Duursma

References

Wang W.M., Li Z.L. & Su H.B. (2007). Comparison of leaf angle distribution functions: Effects on extinction coefficient and fraction of sunlit foliage. Agricultural and Forest Meteorology, 143, 106-122.

See Also

fitdistribution, fitalldistributions

Examples


# Some leaf angle data:
data(eteret)

# Fit the ellipsoidal distribution:
f <- fitdistribution(eteret, "ellipsoid")
f

# Standard plot, histogram with fitted density:
plot(f)


Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LeafAngle)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LeafAngle/fitdistribution.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fitdistribution
> ### Title: Fits a leaf angle distribution
> ### Aliases: fitdistribution
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> # Some leaf angle data:
> data(eteret)
> 
> # Fit the ellipsoidal distribution:
> f <- fitdistribution(eteret, "ellipsoid")
> f
----- Leaf angle distribution -----

Distribution: ellipsoid 
Fit with: Log-likelihood 
Log-likelihood = -3985.601 
AIC = 7973.202 
Parameter X = 0.7127885 
> 
> # Standard plot, histogram with fitted density:
> plot(f)
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>