spider (version 1.5.0)

paa: Population Aggregate Analysis

Description

Conducts population aggregate analysis over a matrix of characters of interest.

Usage

paa(data, sppVector)

Arguments

data

A data matrix with columns as characters and rows as individuals.

sppVector

The species vector. See sppVector.

Value

A matrix with species as rows and characters as columns. Cells give the character state of each species if fixed, or "poly" if the character is polymorphic.

Details

When used on DNA sequences, the function treats gaps as seperate characters.

References

Sites, J. W. J., & Marshall, J. C. (2003). Delimiting species: a Renaissance issue in systematic biology. _Trends in Ecology and Evolution_ *18* (9), 462-470.

Examples

# NOT RUN {
#Create some exemplar data
u <- sample(c(0,1), 16, replace=TRUE)
v <- rep(c(0,1), rep(8,2))
x <- rep(c(1,0), rep(8,2))
y <- sample(c(0,1), 16, replace=TRUE)
z <- rep(c(1,0), rep(8,2))

dat <- cbind(u,v,x,y,z)
popn <- rep(c("A","B", "C", "D"), rep(4,4))

paa(dat, popn)

#Use on DNA sequences
data(anoteropsis)
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"), 
	function(x) paste(x[1], x[2], sep="_"))

paa(as.character(anoteropsis), anoSpp)

# }