poppr (version 1.0.5)

bruvo.boot: Create a tree using Bruvo's Distance with non-parametric bootstrapping.

Description

Create a tree using Bruvo's Distance with non-parametric bootstrapping.

Usage

bruvo.boot(pop, replen = c(1), sample = 100, tree = "upgma",
  showtree = TRUE, cutoff = NULL, quiet = FALSE, ...)

Arguments

pop

a genind object

replen

a vector of integers indicating the length of the nucleotide repeats for each microsatellite locus.

sample

an integer indicated the number of bootstrap replicates desired.

tree

choose between "nj" for neighbor-joining and "upgma" for a upgma tree to be produced.

showtree

logical if TRUE, a tree will be plotted with nodelabels.

cutoff

integer the cutoff value for bootstrap node label values (between 0 and 100).

quiet

logical defaults to FALSE. If TRUE, a progress bar and messages will be supressed.

...

any argument to be passed on to boot.phylo. eg. quiet = TRUE.

Value

• a tree with nodelables

References

Ruzica Bruvo, Nicolaas K. Michiels, Thomas G. D'Souza, and Hinrich Schulenburg. A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level. Molecular Ecology, 13(7):2101-2106, 2004.

See Also

nancycats, upgma, nj, boot.phylo, nodelabels, na.replace, missingno.

Examples

# Please note that the data presented is assuming that the nancycat dataset
# contains all dinucleotide repeats, it most likely is not an accurate
# representation of the data.

# Load the nancycats dataset and construct the repeat vector.
data(nancycats)
ssr <- rep(2, 9)

# Analyze the 1st population in nancycats

bruvo.boot(popsub(nancycats, 1), replen = ssr)