poppr (version 1.1.5)

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 = 1, add = TRUE, loss = TRUE, 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.

add

if TRUE, genotypes with zero values will be treated under the genome addition model presented in Bruvo et al. 2004.

loss

if TRUE, genotypes with zero values will be treated under the genome loss model presented in Bruvo et al. 2004.

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 suppressed.

...

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

Value

• a tree of class phylo 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

bruvo.dist, 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)