Underlying code for DateLife service

AllMatching | Are all desired taxa in the patristic.matrix? |

BindMatrices | Convert list of patristic matrices to a 3D array |

CalculateOverlapTable | Create an overlap table |

CleanChronogram | Clean up some issues with OToL chronograms |

ConvertSpacesToUnderscores | Convert spaces to underscores in trees |

ConvertUnderscoresToSpaces | Convert underscores to spaces in trees |

CreateContributorCache | Create a cache from Open Tree of Life |

CreateTreeBaseCache | Create a cache from TreeBase |

EstimateDates | Core function to input a vector of species, newick string, or... |

FindMatchingStudyIndex | Find the index of relevant studies in a opentree_chronograms... |

GetAge | Get time of MRCA from patristic matrix |

GetAges | Get vector of MRCA from list of patristic matrices |

GetAllCalibrations | Get all calibrations given trees in database |

GetBoldOToLTree | Use Barcode of Life data to get branch lengths on the OToL... |

GetFilteredResults | Go from a vector of species, newick string, or phylo object... |

GetOToLChronograms | Get all chronograms from Open Tree of Life |

GetSubsetArrayDispatch | Figure out which subset function to use |

HasBrlen | Check for branch lengths in a tree |

IsGoodChronogram | Check to see that a chronogram is valid |

PadMatrix | Function to fill in empty cells in a patristic matrix for... |

PatristicMatrixToNewick | Convert patristic matrix to a newick string |

PatristicMatrixToTree | Convert patristic matrix to a phylo object |

ProcessInput | Cleans taxon names from input character vector, phylo object... |

ProcessResultsList | Take results.list and process it |

ReorderMatrix | Function to reorder a matrix so that row and column labels... |

run | Core function to generate results |

RunSDM | Function to compute the SDM supertree Criscuolo et al. 2006 |

SaveOToLChronograms | Save all chronograms from Open Tree of Life |

SummarizeResults | Summarize a filtered results list from GetFilteredResults... |

SummaryPatristicMatrixArray | Summarize patristic matrix array (by default, median) |

TabulateRelevantAuthors | Return the relevant authors for a set of studies |

TabulateRelevantCurators | Return the relevant curators for a set of studies |

UnpadMatrix | Function to remove missing taxa |

UseAllCalibrations | Use all calibrations given trees in database to date a tree |

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