Description Usage Arguments Note Note Author(s)

View source: R/phrapl-utilities.R

This function calculates weights for a tree or set of trees (typically subsampled trees) based on the degeneracy of tip lables (i.e., the proportion of times that permuting labels across a tree results in the same topology). These weights are applied during a grid or heuristic search in phrapl to obtain a more accurate estimate of the log likelihood of an observed tree given trees expected under a given model.

1 | ```
GetPermutationWeightsAcrossSubsamples(popAssignments,observedTrees)
``` |

`popAssignments` |
A list of vectors (typically only one vector will be specified) that define the number of tips per population included in the observed trees (usually these will be subsampled trees). |

`observedTrees` |
Multiphylo object containing the subsampled trees (outputted from PrepSubsampling) |

Because this function exhaustively permutes all possible tip lables across a tree, it can take a long time for large subsampled trees. For more information, please see the user manual.

For more information, please see the user manual.

Nathan Jackson & Brian O'Meara

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