barcode.gap {sidier}

Barcode gap identification

Description

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

Usage

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

Arguments

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.

Value

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.

Author(s)

A.J. Muñoz-Pajares

See Also

barcode.summary

Examples

# 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)