Description Usage Arguments Value Author(s) See Also Examples
This function uses hierarchical clustering on principal components output by treescape
to identify groups of similar trees. Clustering relies on hclust
, using Ward's method by default.
1 2 | findGroves(x, method = "treeVec", nf = NULL, clustering = "ward.D2",
nclust = NULL, ...)
|
x |
an object of the class multiPhylo or the output of the function |
method |
(ignored if x is from |
nf |
(ignored if x is from |
clustering |
a character string indicating the clustering method to be used; defaults to Ward's method; see argument |
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 |
A list containing:
groups: a factor defining groups of trees
treescape: the output of treescape
Thibaut Jombart thibautjombart@gmail.com
Michelle Kendall michelle.louise.kendall@gmail.com
plotGroves
to display results
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | if(require("adegenet") && require("adegraphics")){
## load data
data(woodmiceTrees)
## run findGroves: treescape+clustering
res <- findGroves(woodmiceTrees, nf=5, nclust=6)
## plot results on first 2 axes
PCs <- res$treescape$pco$li
s.class(PCs, fac=res$groups, col=funky(6))
## using plotGroves
plotGroves(res)
}
|
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