ARES-package {ARES}R Documentation

Allelic richness estimation, with extrapolation beyond the sample size

Description

Allows to easily generates and plot an allelic richness accumulation curve. This curve shows the expected number of unique alleles in a population when taking a sample of individuals, ranging from one to maxsize individuals. It takes a binary data matrix as input, showing the presence of alleles per individual, and gives an accumulation curve (mean with 95% confidence bounds) back. The total number of individuals present in the input data can be smaller then maxsize. The package contains three functions that can be called by users: aresCalc ,aresPlot, and read.genepop.

Details

Package: ARES
Type: Package
Version: 1.1
Date: 2006-11-03
License: GPL 2 or newer

Author(s)

Emiel van Loon and Scott Davis, based on code by Chang Xuan Mao Maintainer: Emiel van Loon <vanloon@uva.nl>

References

Colwell RK, Mao CX, Chang J (2004) Interpolating, extrapolating and comparing incidence-based species accumulation curves. Ecology, 85, 2717-2727.

Mao CX, Colwell RK, Chang J (2006) Estimating the species accumulation curve using mixtures. Biometrics, 61, 433-441.

van Loon EE, Cleary DFR, Fauvelot C (2006) ARES: software to compare allelic richness between uneven samples. Molecular Ecology Notes, (in review)

Examples

# allelic richness of the butterfly Drupadia theda (Felder),  
# at a study site B1 in the year 1998 compared to that in 2000

data(butterfly_borneo)

b198 <- aresCalc(bb198,bootsize=4,maxsize=60)
aresPlot(b198, T="1998, B1")

b100 <- aresCalc(bb100,bootsize=4,maxsize=60)
aresPlot(b100, T="2000, B1")

# note!!! these examples use a very small bootstrap size (for speed of display).
#  A more realistic size is bootsize=200.


[Package ARES version 1.2-3 Index]