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

View source: R/rank.partitionedRAD.R

This function takes output from `match.lnL.to.trees`

and scores trees as
favored or disfavored for all loci that satisfy the criteria specified

1 2 3 4 | ```
rank.partitionedRAD(radMat, minTrees = 10,
min.overall.diff.lnL = 5,
threshold.lnL = 2,
discardDoubleCounts = TRUE)
``` |

`radMat` |
matrix output from |

`minTrees` |
integer, minimum number of unique trees required per locus |

`min.overall.diff.lnL` |
minimum log-likelihood difference required between the most poorly- supported tree and the best supported tree for each locus |

`threshold.lnL` |
the log-likelihood window for binning a tree into favored or disfavored |

`discardDoubleCounts` |
determines whether that place any tree within both the favored and
disfavored bins should be counted ( |

This function works by first filtering loci by the minimum number of trees and the
overall range in log-likelihood, then binning trees into supported if they are within
`threshold.lnL`

of the best-supported tree for each locus, and disfavored if they
are within `threshold.lnL`

of the least supported tree for each locus. Overlapping
trees can occur when the range in log-likelihood is set to less than twice the threshold
log-likelihood or quite near it.

A list composed of 7 matrices and one numeric vector. The matrices all have loci as the rows and trees as the columns:

`bestMat` |
boolean; which trees are supported by which loci |

`worstMat` |
boolean; which trees are disfavored by which loci |

`doubleCountMat` |
boolean; which trees are double-counted by which loci |

`radMat` |
the final likelihood matrix corresponding with |

`radMat.preLnLDiff` |
the likelihood matrix before filtering by lnL range |

`radMat.preMinTrees` |
the likelihood matrix before filtering by minimum number of trees |

`radMat.preDoubleCounts ` |
the likelihood matrix before filtering by double counts |

`params` |
the analysis parameters, in this order: minTrees, min.overall.diff.lnL, threshold.lnL, discardDoubleCounts |

Andrew Hipp

Hipp A.L., Eaton D.A.R., Cavender-Bares J., Fitzek E., Nipper R. & Manos P.S. (Accepted pending revision). A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS ONE.

`match.lnL.to.trees`

,
`plot.rankedPartitionedRAD`

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