barcode.gap: Barcode gap identification
In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

Description Usage Arguments Value Author(s) See Also Examples

Identifies barcode gaps based on representing intra- and interspecific distances. Species above the 1:1 line are considered to show a barcode gap.

1 2	barcode.gap(summary=NULL,stat.intra="max",stat.inter="min", xlab=NULL, ylab=NULL, legend=TRUE, lab.nodes="nogap")

`summary`	a list produced by `barcode.summary`. From this list, the maximum intraspecific and the minimum interspecific distances per species are represented. To use any other intra- and interspecific distance, use the "inter" and "intra" options.
`stat.intra`	a string, the inter-specific statistic used to estimate the quotient interspecific/intraspecific. Accepted values are "max", "min", "median", and "mean"
`stat.inter`	a string, the inter-specific statistic used to estimate the quotient interspecific/intraspecific. Accepted values are "max", "min", "median", and "mean".
`xlab`	a string, the x-axis label
`ylab`	a string, the y-axis label
`legend`	a logic, to show information about species showing and lacking barcode within the plot
`lab.nodes`	a string to select the name of species to be represented in the plot: "gap" to represent species showing barcode gap; "nogap" to represent species lacking barcode gap; "all" for representing all species names. Other value will represent no names.

A list with two elements:

`no.barcode.gap`	a matrix containing the name of the species lacking barcode gap and their mean intra- and interspecific distances.
`barcode.gap`	a matrix containing the name of the species showing barcode gap and their mean intra- and interspecific distances.

A.J. Muñoz-Pajares

barcode.summary

# my.dist<-matrix(abs(rnorm(100)),ncol=10,
# dimnames=list(paste("sp",rep(1:5,2),sep=""),
# paste("sp",rep(1:5,2),sep="")))
# my.dist<-as.matrix(as.dist(my.dist))
# sum<-barcode.summary(my.dist)
# barcode.gap(sum)