Assign regimes on a tree given a set of starting branches

PCMTreeSetRegimes(tree, nodes, regimes = as.integer(1:(length(nodes) +
  1)), inplace = TRUE)

Arguments

tree

a phylo object

nodes

a character vector containing tip or node labels or an integer vector denoting tip or internal nodes in tree - the regimes change at the start of the branches leading to these nodes.

regimes

an integer or character vector of length equal to length(nodes) + 1 containing the regime-names to be assigned for each regime. If NULL the regime names will be the integers 1:(length(nodes) + 1).

inplace

a logical indicating if the change should be done to the tree in the calling environment (TRUE) or a copy of the tree with set edge.regime member should be returned (FALSE). Default is TRUE.

Value

If inplace is TRUE nothing, otherwise a copy of the tree with set edge.regime member.

Details

It is assumed that each regime "paints" a linked subset of branches on a tree. Thus, each regime is fully described by its starting branch. The descendant branches inherit this regime until reaching a tip or a node that is present in the nodes parameter.

See also