Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/BioGeoBEARS_simulate_v1.R

This function extracts the ML states from the results
list produced by `bears_2param_standard_fast`

or a similar ML search function.

1 | ```
get_ML_states(relprobs_matrix, unlist_TF = TRUE)
``` |

`relprobs_matrix` |
A relative probabilities matrix
returned by |

`unlist_TF` |
Unlist the output? Default TRUE. |

Currently, the scaled conditional probabilities are used
to determine the optimum states. However, this is not
strictly correct, as these use only tips-down information
(Felsenstein (2004); see also this post by Revell:
http://blog.phytools.org/2013/03/marginal-ancestral-state-reconstruction.html).
This is what `LAGRANGE`

seems to do when reporting
ancestral states, also (personal observation, perhaps
imperfect, especially if the scaled conditional
likelihoods and the marginal ancestral state
probabilities turn out to be very close). What is desired
is the marginal ancestral state reconstructions. Most
authors discuss ML ancestral state reconstruction as
being a matter of re-rooting the tree at each node,
yielding the marginal estimate for that node, conditional
on the rest of the tree. However, this procedure assumes
a time-reversible model on both branches and cladogenesis
events, and we have neither in biogeography. Probably,
the solution is just an up-pass from the root,
calculating the probabilities on the forward model and
multiplying by likelihoods from the downpass. However,
this has not yet been implemented.

`inf_statesvec`

The inferred vector of states.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster http://blog.phytools.org/2013/03/marginal-ancestral-state-reconstruction.html https://code.google.com/p/lagrange/

Felsenstein2004

Matzke_2012_IBS

`get_ML_probs`

,
`bears_2param_standard_fast`

,
`get_ML_state_indices`

1 | ```
testval=1
``` |

```
Loading required package: rexpokit
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase
Attaching package: 'phylobase'
The following object is masked from 'package:ape':
edges
```

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