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,
  root = NULL,
  ...
)

Arguments

pop: a genind or genclone 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: any function that can generate a tree from a distance matrix. Default is upgma.
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.
root: logical This is a parameter passed on to boot.phylo. If the tree argument produces a rooted tree (e.g. "upgma"), then this value should be TRUE. If it produces an unrooted tree (e.g. "nj"), then the value should be FALSE. By default, it is set to NULL, which will assume an unrooted phylogeny unless the function name contains "upgma".
...: any argument to be passed on to boot.phylo. eg. quiet = TRUE.

Value

a tree of class phylo with nodelables

Details

This function will calculate a tree based off of Bruvo's distance and then utilize boot.phylo to randomly sample loci with replacement, recalculate the tree, and tally up the bootstrap support (measured in percent success). While this function can take any tree function, it has native support for two algorithms: nj and upgma. If you want to use any other functions, you must load the package before you use them (see examples).

Note

Please refer to the documentation for bruvo.dist for details on the algorithm. If the user does not provide a vector of appropriate length for replen , it will be estimated by taking the minimum difference among represented alleles at each locus. IT IS NOT RECOMMENDED TO RELY ON THIS ESTIMATION.

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.

Author

Zhian N. Kamvar, Javier F. Tabima

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)
#> 
#> Bootstrapping...
#> (note: calculation of node labels can take a while even after the progress bar is full)
#> 
#> 
Running bootstraps:       100 / 100
#> Calculating bootstrap values... done.

#> 
#> Phylogenetic tree with 10 tips and 9 internal nodes.
#> 
#> Tip labels:
#>   N215, N216, N217, N218, N219, N220, ...
#> Node labels:
#>   100, 29, 18, 75, 48, 53, ...
#> 
#> Rooted; includes branch lengths.

# \dontrun{

# Always load the library before you specify the function.
library("ape")

# Estimate the tree based off of the BIONJ algorithm.

bruvo.boot(popsub(nancycats, 9), replen = ssr, tree = bionj)
#> 
#> Bootstrapping...
#> (note: calculation of node labels can take a while even after the progress bar is full)
#> 
#> 
Running bootstraps:       100 / 100
#> Calculating bootstrap values... done.

#> 
#> Phylogenetic tree with 9 tips and 7 internal nodes.
#> 
#> Tip labels:
#>   N104, N105, N106, N107, N108, N109, ...
#> Node labels:
#>   NA, 18, 27, 28, 28, 60, ...
#> 
#> Unrooted; includes branch lengths.

# Utilizing  balanced FastME
bruvo.boot(popsub(nancycats, 9), replen = ssr, tree = fastme.bal)
#> 
#> Bootstrapping...
#> (note: calculation of node labels can take a while even after the progress bar is full)
#> 
#> 
Running bootstraps:       100 / 100
#> Calculating bootstrap values... done.

#> 
#> Phylogenetic tree with 9 tips and 7 internal nodes.
#> 
#> Tip labels:
#>   N104, N105, N106, N107, N108, N109, ...
#> Node labels:
#>   NA, 29, 29, 24, 62, 22, ...
#> 
#> Unrooted; includes branch lengths.

# To change parameters for the tree, wrap it in a function.
# For example, let's build the tree without utilizing subtree-prune-regraft

myFastME <- function(x) fastme.bal(x, nni = TRUE, spr = FALSE, tbr = TRUE)
bruvo.boot(popsub(nancycats, 9), replen = ssr, tree = myFastME)
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> 
#> Bootstrapping...
#> (note: calculation of node labels can take a while even after the progress bar is full)
#> 
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> Warning: option 'tbr = TRUE' was ignored: see ?fastme.bal
#> 
Running bootstraps:       100 / 100
#> Calculating bootstrap values... done.

#> 
#> Phylogenetic tree with 9 tips and 7 internal nodes.
#> 
#> Tip labels:
#>   N104, N105, N106, N107, N108, N109, ...
#> Node labels:
#>   NA, 15, 7, 23, 66, 94, ...
#> 
#> Unrooted; includes branch lengths.

# }