rule {sidier} | R Documentation |
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 |
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.
Author(s)
A.J. Muñoz-Pajares
Examples
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)