Inferring jumps (task inferJumps)

This is an alternative to task "infer" when the user is interested in inferring only the phylogenetic positions of the jumps, and not the other jump parameters. To infer jumps with levolution, specify task=inferJumps. Then one needs to specify the mandatory parameters: tree, traits, rootState, brownVar, lambda, and alpha. An example command line to infer jump parameters from a tree file myTree.tree and a traits file myTraits.traits might look like this:

./levolution task=inferJumps tree=myTree.tree traits=myTraits.traits rootState=10 brownVar=10 alpha=100 lambda=3

The tree file has to be in newick format. The traits file consist of two columns with no header. The first column has the tree tips names (the same as in the tree file), and the second column has the trait values.

If one desires to change the MCMC settings for this jump-location estimation step one can also use the arguments numNVecsEB, thinningEB, and burninEB.