View source: R/permute_all_uncertainties.r
permute_all_uncertainties | R Documentation |
Given a set of discrete states, will permute all possible uncertainity combinations of those states.
permute_all_uncertainties(single_states)
single_states |
A vector of single states (e.g., 0, 1, 2 etc.). |
This function solves a simple phylogenetic combinatorics problem - what are all the possible outcomes for a character to be in given uncertainties are allowed?
For example, for three states (0, 1, 2) there are four possible uncertainties: 0/1, 0/2, 1/2 and 0/1/2.
If the user is instead only interested in the size of this state space, this is simply given by 2^N - N - 1, where N is the number of single states. Thus, the first several outcomes are:
---------------------------------- | N states | N possible outcomes | ---------------------------------- | 2 | 1 | | 3 | 4 | | 4 | 11 | | 5 | 26 | | 6 | 57 | | 7 | 120 | | 8 | 247 | | 9 | 502 | | 10 | 1,013 | | 11 | 2,036 | | 12 | 4,083 | | 13 | 8,178 | | 14 | 16,369 | ----------------------------------
Note that this function is really designed for internal use, but may have value to some users and so is available "visibly" here.
A vector of all possible uncertainty states.
Graeme T. Lloyd graemetlloyd@gmail.com
make_costmatrix and permute_all_polymorphisms
# Get all possible states for the character 0, 1, and 2:
permute_all_uncertainties(single_states = 0:2)
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