average_tr_tips

Tips that are older than
  <code>fossils_older_than</code> will be excluded from the tips
  that are going to be averaged. This is not currently set
  to 0, because Newick files can have slight precision
  issues etc. that mean not all tips quite come to zero
  (which is why you need <code><a rd-options="" href="/link/average_tr_tips?package=BioGeoBEARS&version=0.2.1" data-mini-rdoc="BioGeoBEARS::average_tr_tips">average_tr_tips</a></code> in
  the first place!). Obviously you should be cautious about
  the value of , depending on the absolute timescale of
  your tree. Make sure you do not inappropriately average
  in fossils!!

fossils_older_than


  When you have a digitized tree, or other slightly uneven
  source tree, average the tips to get them all to line up
  at 0 my before present.  This makes an ultrametric tree
  if and only if there are no fossil tips in the tree.


BioGeoBEARS allows probabilistic inference of both historical biogeography (ancestral geographic ranges on a phylogeny) as well as comparison of different models of range evolution.  It reproduces the model available in LAGRANGE (Ree and Smith 2008), as well as making available numerous additional models. For example, LAGRANGE as typically run has two free parameters, d (dispersal rate, i.e. the rate of range addition along a phylogenetic branch) and e (extinction rate, really the rate of local range loss along a phylogenetic branch). LAGRANGE also has a fixed cladogenic model which gives equal probability to a number of allowed range inheritance events, e.g.: (1) vicariance, (2) a new species starts in a subset of the ancestral range, (3) the ancestral range is copied to both species; in all cases, at least one species must have a starting range of size 1.  LAGRANGE assigns equal probability to each of these events, and zero probability to other events.  BioGeoBEARS adds an additional cladogenic event: founder-event speciation (the new species jumps to a range outside of the ancestral range), and also allows the relative weighting of the different sorts of events to be made into free parameters, allowing optimization and standard model choice procedures to pick the best model. The relative probability of different descendent range sizes is also parameterized and thus can also be specified or estimated.  The flexibility available in BioGeoBEARS also enables the natural incorporation of (1) imperfect detection of geographic ranges in the tips, and (2) inclusion of fossil geographic range data, when the fossils are tips on the phylogeny. Bayesian analysis has been implemented through use of the "LaplacesDemon" package, however this package is now maintained off of CRAN, so its usage is not formally included in BioGeoBEARS at the current time.  CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it!  Type: citation(package="BioGeoBEARS") to get the citation information.

average_tr_tips: Average the heights of (non-fossil) tips to make ultrametric-ish.

Description

Usage

Arguments

Value

Details

References

See Also

Examples