Description Usage Arguments Examples
Sub-lineage identification using a phylogentic tree with branch lengths indicating SNP distance.
1 |
tree |
a phylo object |
thresh |
SNP threshold for sub-lineage identification. |
rthreshold |
The threhold number of ancestral nodes to the root each sub-lineage must have if they are to be declared as major sub-lineages |
quiet |
whether or not to print out extra information (default=FALSE) |
1 2 3 | tree.file.name <- system.file("extdata", "pyjar.staph_ST2371_45_re_itol_7079_1_6_root.joint.tre", package = "rPinecone")
tree <- phytools::read.newick(tree.file.name)
pinecone(tree, 2, 3)
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