aresCalc {ARES}R Documentation

Allelic richness estimation, with extrapolation beyond the sample size

Description

Generates 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 till 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.

Usage

aresCalc(rawdata, bootsize = NULL, maxsize = NULL)

Arguments

rawdata a binary data matrix with columns representing different individuals and rows representing different alleles
bootsize the number of bootstrap runs to be made, for calculating confidence bounds (typically between 100 and 1000)
maxsize the number of individuals to where the accumulation curve has to be calculated

Value

The function returns a table of 3 columns and maxsize rows. The first column holds the mean (named esti), the second the lower 97.5 % conf. bound (named lwr) and the third the upper 97.5% conf. bound (named upr) The output can be visualised by the function aresPlot.

Author(s)

Emiel van Loon, based on code by Chang Xuan Mao

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")

# display the results of aresCalc as a table in the R console
b100

# write the results of aresCalc to a csv-file
write.csv(b100, file = "b100.csv")

# 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]