Identify clusters of similar trees

This function uses hierarchical clustering on principal components output by treespace to identify groups of similar trees. Clustering relies on hclust, using Ward's method by default.

findGroves(
  x,
  method = "treeVec",
  nf = NULL,
  clustering = "ward.D2",
  nclust = NULL,
  ...
)

Arguments

x

an object of the class multiPhylo or the output of the function treespace

method

(ignored if x is from treespace) this specifies a function which outputs the summary of a tree in the form of a vector. Defaults to treeVec.

nf

(ignored if x is from treespace) the number of principal components to retain

clustering

a character string indicating the clustering method to be used; defaults to Ward's method; see argument method in ?hclust for more details.

nclust

an integer indicating the number of clusters to find; if not provided, an interactive process based on cutoff threshold selection is used.

...

further arguments to be passed to treespace

Value

A list containing:

• groups: a factor defining groups of trees

• treespace: the output of treespace

See also

plotGroves to display results

Author

Thibaut Jombart thibautjombart@gmail.com

Michelle Kendall michelle.louise.kendall@gmail.com

Examples

if(require("adegenet") && require("adegraphics")){
## load data
data(woodmiceTrees)

## run findGroves: treespace+clustering
res <- findGroves(woodmiceTrees, nf=5, nclust=6)

## plot results on first 2 axes
PCs <- res$treespace$pco$li
s.class(PCs, fac=res$groups, col=funky(6))

## using plotGroves
plotGroves(res)
}
#> Loading required package: adegenet
#> 
#>    /// adegenet 2.1.10 is loaded ////////////
#> 
#>    > overview: '?adegenet'
#>    > tutorials/doc/questions: 'adegenetWeb()' 
#>    > bug reports/feature requests: adegenetIssues()
#> 
#> 
#> Attaching package: ‘adegenet’
#> The following object is masked from ‘package:treespace’:
#> 
#>     .render.server.info
#> Loading required package: adegraphics
#> 
#> Attaching package: ‘adegraphics’
#> The following objects are masked from ‘package:ade4’:
#> 
#>     kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
#>     s.label, s.logo, s.match, s.traject, s.value, table.value,
#>     triangle.class
#> The following object is masked from ‘package:ape’:
#> 
#>     zoom