ARES-package {ARES} | R Documentation |
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
.
Package: | ARES |
Type: | Package |
Version: | 1.1 |
Date: | 2006-11-03 |
License: | GPL 2 or newer |
Emiel van Loon and Scott Davis, based on code by Chang Xuan Mao Maintainer: Emiel van Loon <vanloon@uva.nl>
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)
# 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.