document load.outer.tree() for importation

[davidchampredon]

@ArtPoon, could you please add an example in the documentation of load.outer.tree() when the outer tree has not been simulated by twt but is instead imported from another source (like my ABM)?

I used to do somthing like the code below in a recent twt version but some functions have disappeared and everything I try fails. Thanks!

settings <- yaml.load_file('../data/sampled-hosts-1.yaml')
m     <- Model$new(settings)
outer.tree <- ape::read.tree('../data/transm.nwk')
evlog <- eventlog.from.tree(tree = outer.tree)
inner <- sim.inner.tree(obj = m, e = evlog)

[ArtPoon]

Sorry for the confusion. I've been reworking that function so the documentation no longer fits. I'll try to get to this today.

[ArtPoon]

The decision we reached in #107 was to use YAML to specify an outer tree generated by another program, so eventlog.from.tree is deprecated code. (I've also renamed it to attach.tree.)

[ArtPoon]

You should be able to load your transmission tree as as YAML file with load.outer.tree