barcode.summary: Summary of the inter- and intraspecific distances

In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

Description

For every species, provides the minimum, maximum, mean and median values of inter- and intraspecific distances.

Usage

barcode.summary(dismat=NULL,save.distances=FALSE,folder.name="distance_matrices")

Arguments

dismat	a symmetric matrix containing the pairwise genetic distances between individual sequences
save.distances	a logic, "TRUE" to save the pairwise distances estimated per species (one file per species)
folder.name	a string, if save.distance=TRUE, the name of the folder to save distances

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

See Also

barcode.gap

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))
# barcode.summary(my.dist)

sidier documentation built on June 25, 2021, 5:10 p.m.