Man pages for phylotastic/datelife
Underlying code for DateLife service

AllMatchingAre all desired taxa in the patristic.matrix?
BindMatricesConvert list of patristic matrices to a 3D array
CalculateOverlapTableCreate an overlap table
CleanChronogramClean up some issues with OToL chronograms
ConvertSpacesToUnderscoresConvert spaces to underscores in trees
ConvertUnderscoresToSpacesConvert underscores to spaces in trees
CreateContributorCacheCreate a cache from Open Tree of Life
CreateTreeBaseCacheCreate a cache from TreeBase
EstimateDatesCore function to input a vector of species, newick string, or...
FindMatchingStudyIndexFind the index of relevant studies in a opentree_chronograms...
GetAgeGet time of MRCA from patristic matrix
GetAgesGet vector of MRCA from list of patristic matrices
GetAllCalibrationsGet all calibrations given trees in database
GetBoldOToLTreeUse Barcode of Life data to get branch lengths on the OToL...
GetFilteredResultsGo from a vector of species, newick string, or phylo object...
GetOToLChronogramsGet all chronograms from Open Tree of Life
GetSubsetArrayDispatchFigure out which subset function to use
HasBrlenCheck for branch lengths in a tree
IsGoodChronogramCheck to see that a chronogram is valid
PadMatrixFunction to fill in empty cells in a patristic matrix for...
PatristicMatrixToNewickConvert patristic matrix to a newick string
PatristicMatrixToTreeConvert patristic matrix to a phylo object
ProcessInputCleans taxon names from input character vector, phylo object...
ProcessResultsListTake results.list and process it
ReorderMatrixFunction to reorder a matrix so that row and column labels...
runCore function to generate results
RunSDMFunction to compute the SDM supertree Criscuolo et al. 2006
SaveOToLChronogramsSave all chronograms from Open Tree of Life
SummarizeResultsSummarize a filtered results list from GetFilteredResults...
SummaryPatristicMatrixArraySummarize patristic matrix array (by default, median)
TabulateRelevantAuthorsReturn the relevant authors for a set of studies
TabulateRelevantCuratorsReturn the relevant curators for a set of studies
UnpadMatrixFunction to remove missing taxa
UseAllCalibrationsUse all calibrations given trees in database to date a tree
phylotastic/datelife documentation built on Nov. 10, 2017, 1:49 a.m.