mcmc2anc: Ancestral character reconstruction from an MCMC sample

In dosreislab/mcmc3r: Tools to work with MCMCtree

Ancestral character reconstruction from an MCMC sample

Description

Obtain the ancestral reconstruction of characters from an MCMC sample using Felsenstein (1973) model of continuous character evolution.

Usage

mcmc2anc(tree, M, mcmc, time.name, rate.name, tip.ages = NULL)

Arguments

tree	a rooted, strictly bifurcating phylogeny
M	s x k matrix of k continuous morphological measurements for s species
mcmc	data frame with MCMC output from MCMCtree
time.name	character vector of length one
rate.name	character vector of length one
tip.ages	numeric, the ages of the terminal taxa in the tree

Details

The function first calculates the mean of divergence times and morphological rates in the MCMC sample. These are used to reconstruct the branch lengths in units of morphological evolution, and then Eq. (7) in Felsenstein (1973) is used to calculate the ancestral reconstruction on the tree.

Note time.name is the name format used for the node ages in the MCMC dataframe, usually of the form time.name = "t_". Similarly rate.name is the name format used in the MCMC sample for the rates, of the form rate.name = "r_g1_" where the subscript in "g" must be the partition number containing the morphological rates. Note tree must be the same used by MCMCtree when generating the MCMC sample, right down to its Newick representation. Taxon names in tree and M must match.

Value

A n x k matrix with the ancestral reconstruction for the k characters at the n internal nodes of the phylogeny.

Author(s)

Mario dos Reis

References

Felsenstein J (1973) Maximum-likelihood estimation of evolutionary trees from continuous characters. Am J Hum Genet, 25: 471–492.

See Also

write.morpho

Examples

data(carnivores) 
# calculate tip ages correctly, as they're needed by the function:
tips_info <- strsplit(carnivores$tree$tip.label, "\\^" )
back.ages <- as.numeric(unlist(tips_info)[seq(from=2, to=2*19, by=2)])
back.ages <- max(back.ages) - back.ages 
C <- carnivores$C.proc
rownames(C) <- rownames(carnivores$M)
recM = mcmc2anc(carnivores$tree, C, mcmc=carnivores$mcmc, time.name="t_", 
       rate.name="r_g1_", tip.ages=back.ages)

x <- seq(1, 87, by=3); y <- seq(2, 87, by=3)
# Plot landmarks for the 19 carnivores:
plot(carnivores$C.proc[,x], carnivores$C.proc[,y], pch='+', cex=.5)
# plot ancestral reconstruction at the root (node 20):
points(recM["20",x], recM["20",y], pch=19, col="red")
# mean shape
mS <- apply(carnivores$C.proc, 2, mean)
points(mS[x], mS[y], pch=19, col="blue")

# Convert reconstruction to an array, as is the standard in
# morphometrics software
## Not run: 
recA <- matrix2array(recM, 3)
options(rgl.printRglwidget = TRUE)
rgl::plot3d(recA[,,"20"], ty='s', size=2, col="red", aspect=FALSE)

## End(Not run)

dosreislab/mcmc3r documentation built on March 29, 2024, 6:45 p.m.