simstates_to_probs_of_each_area: Convert simulated states to probabilities of each area

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

View source: R/BioGeoBEARS_simulate_v1.R

Description

Basically this function assigns probability 1 to occupied areas according to the simulated state for a node, and probability 0 for the other areas. These data – the simulated truth – can then be compared to the inferred probabilities of presence in each area, from infprobs_to_probs_of_each_area.

Usage

1
2
  simstates_to_probs_of_each_area(simulated_states_by_node,
    states_list, relprobs_matrix)

Arguments

simulated_states_by_node

The simulated states by node (0-based indices).

states_list

A list of the possible states/geographic ranges, in 0-based index form.

relprobs_matrix

A relative probabilities matrix returned by bears_2param_standard_fast or a similar function. The user should specify WHICH matrix in the results_object – i.e., scaled conditional likelihoods on downpass or uppass, or actual marginal probabilities of ancestral states. (The latter is the main thing of interest.) This specification is done via e.g. relprobs_matrix = results_object$relative_probs_of_each_state_at_branch_top_AT_node_DOWNPASS..

Value

area_probs The probability of presence in each area.

Note

Go BEARS!

Author(s)

Nicholas J. Matzke matzke@berkeley.edu

References

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster

Matzke_2012_IBS

See Also

simulate_biogeog_history, infprobs_to_probs_of_each_area

Examples

1
testval=1

Example output

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

BioGeoBEARS documentation built on May 29, 2017, 8:36 p.m.