Package: TipDatingBeast 1.1-0

TipDatingBeast: Using Tip Dates with Phylogenetic Trees in BEAST

Assists performing tip-dating of phylogenetic trees with BEAST BEAST is a popular software for phylogenetic analysis. The package assists the implementation of various phylogenetic tip- dating tests using BEAST. It contains two main functions. The first one allows preparing date randomization analyses, which assess the temporal signal of a data set. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. The included tutorial provides detailed step-by-step instructions. An expanded description of the package can be found in article: Rieux, A. and Khatchikian, C.E. (2017), TIPDATINGBEAST: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST. Molecular Ecology Resources, 17: 608-613. <onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12603>.

Authors:Adrien Rieux, Camilo Khatchikian

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7 exports 1 stars 2.14 score 47 dependencies 9 mentions 10 scripts 212 downloads

Last updated 5 years agofrom:b23bcc57c3. Checks:OK: 7. Indexed: yes.

Exports:ListTaxaPlotDRTPlotLOOCVRandomClusterRandomDatesTaxaOutTaxonOut

Dependencies:askpassbootcellrangerclassclicpp11crayoncurldata.tableDescToolse1071ExactexpmfansigldgluehmshttrjsonlitelatticelifecyclelmommagrittrMASSMatrixmclustmimemvtnormopensslpillarpkgconfigprettyunitsprogressproxyR6RcppreadxlrematchrlangrootSolverstudioapisysTeachingDemostibbleutf8vctrswithr