MPR {ape}  R Documentation 
This function does ancestral character reconstruction by parsimony as described in Hanazawa et al. (1995) and modified by Narushima and Hanazawa (1997).
MPR(x, phy, outgroup)
x 
a vector of integers. 
phy 
an object of class 
outgroup 
an integer or a character string giving the tip of

Hanazawa et al. (1995) and Narushima and Hanazawa (1997) used Farris's (1970) and Swofford and Maddison's (1987) framework to reconstruct ancestral states using parsimony. The character is assumed to take integer values. The algorithm finds the sets of values for each node as intervals with lower and upper values.
It is recommended to root the tree with the outgroup before the
analysis, so plotting the values with nodelabels
is
simple.
a matrix of integers with two columns named “lower” and “upper” giving the lower and upper values of the reconstructed sets for each node.
Emmanuel Paradis
Farris, J. M. (1970) Methods for computing Wagner trees. Systematic Zoology, 19, 83–92.
Hanazawa, M., Narushima, H. and Minaka, N. (1995) Generating most parsimonious reconstructions on a tree: a generalization of the Farris–Swofford–Maddison method. Discrete Applied Mathematics, 56, 245–265.
Narushima, H. and Hanazawa, M. (1997) A more efficient algorithm for MPR problems in phylogeny. Discrete Applied Mathematics, 80, 231–238.
Swofford, D. L. and Maddison, W. P. (1987) Reconstructing ancestral character states under Wagner parsimony. Mathematical Biosciences, 87, 199–229.
## the example in Narushima and Hanazawa (1997): tr < read.tree(text = "(((i,j)c,(k,l)b)a,(h,g)e,f)d;") x < c(1, 3, 0, 6, 5, 2, 4) names(x) < letters[6:12] (o < MPR(x, tr, "f")) plot(tr) nodelabels(paste0("[", o[, 1], ",", o[, 2], "]")) tiplabels(x[tr$tip.label], adj = 2) ## some random data: x < rpois(30, 1) tr < rtree(30, rooted = FALSE) MPR(x, tr, "t1")