Rev Language Reference
tmrca - Find the time to the most recent common ancestor
Finds the most recent common ancestor (TMRCA) of a clade of taxa on a tree.
Usage
Arguments
| tree : | TimeTree (pass by const reference) |
| The tree variable. | |
| clade : | Clade (pass by value) |
| The clade. | |
| stemAge : | Bool (pass by value) |
| Do we want the stem age or crown age? | |
| Default : FALSE |
Return Type
Example
# let's make up some taxa
taxa = v("horse", "whale", "unicorn", "narwhal")
# convert these to the taxon datatype
for(i in 1:4) { taxa[i] = taxon(taxa[i]) }
# simulate a tree
tau ~ dnUniformTimeTree(rootAge=1, taxa=taxa)
# we also need a molecular substitution model
molecular_model := fnJC(4)
# together these form a continuous time Markov chain over the tree
full_model ~ dnPhyloCTMC(tree=tau, Q=molecular_model, nSites = 100, type="DNA")
# need to make a clade
horned_animals <- clade(taxa[3], taxa[4])
tmrca(tau, horned_animals)
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