sidier (version 4.1.0)

rule: Threshold to discriminate species.

Description

Threshold to discriminate species showing a ratio interspecific/intraspecific distances higher than a given value.

Usage

rule(summary=NULL,rule=NULL,stat.intra="max",
stat.inter="min",pch.intra=16, pch.inter=16,
pch.out=21,col.intra="gray",col.inter="black",
col.out="black",label=F)

Arguments

summary

a list produced by barcode.summary. From this list, the maximum intraspecific and the minimu interspecific distances per species are represented. To use any other intra- and interspecific distance, use the "inter" and "intra" options.

rule

a numeric. Only species showing interspecific distances higher than 'rule' times the intraspecific distances will be considered for threshold estimation.

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".

pch.intra

Either an integer or single character defining the symbol to be used for intraspecific distances. Only species showing a ratio interspecific/intraspecific higher than the value defined by 'rule' are affected by 'pch.intra'.

pch.inter

Either an integer or single character defining the symbol to be used for interspecific distances Only species showing a ratio interspecific/intraspecific higher than the value defined by 'rule' are affected by 'pch.inter'.

pch.out

Either an integer or single character defining the symbol to be used for species showing a ratio interspecific/intraspecific lower than the value defined by 'rule'.

col.intra

Either an integer or string defining the colour for intraspecific distances showing a ratio interspecific/intraspecific higher than the value defined by 'rule'.

col.inter

Either an integer or string defining the colour for interspecific distances showing a ratio interspecific/intraspecific higher than the value defined by 'rule'.

col.out

Either an integer or string defining the colour forspecies showing a ratio interspecific/intraspecific lower than the value defined by 'rule'.

label

a string to set node labels on those species showing a ratio interspecific/intraspecific higher than the value defined ("rule"), on species showing a ratio interspecific/intraspecific higher than the value defined ("norule"), on all species ("all"). Any other value will produce no lable

Value

A list with two elements:

Intraspecific

a matrix containing information about the intraspecific distances.

Interspecific

a matrix containing information about the interspecific distances.

In both cases, the information provided is the minimum, maximum, median, mean, first and third quartile values.

Examples

# NOT RUN {
my.dist<-matrix(c(0,0.3,0.24,0.45,0.23,0.01,0.11,0.34,0.64,0.34,
0.3,0,0.32,0.75,0.65,0.53,0.012,0.52,0.15,0.52,0.24,0.32,
0,0.92,0.36,0.62,0.85,0.008,0.82,0.65,0.45,0.75,0.92,0,
0.22,0.56,0.74,0.46,0.005,0.73,0.23,0.65,0.36,0.22,0,
0.34,0.24,0.42,0.35,0.009,0.01,0.53,0.62,0.56,0.34,0,
0.23,0.73,0.23,0.63,0.11,0.012,0.85,0.74,0.24,0.23,0,
0.25,0.63,0.54,0.34,0.52,0.008,0.46,0.42,0.73,0.25,0,
0.32,0.41,0.64,0.15,0.82,0.005,0.35,0.23,0.63,0.32,0,
0.23,0.34,0.52,0.65,0.73,0.009,0.63,0.54,0.41,0.23,0),
ncol=10,dimnames=list(paste("sp",rep(1:5,2),sep=""),
paste("sp",rep(1:5,2),sep="")))

# rule(barcode.summary(my.dist),rule=10)
# }