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:
TipDatingBeast_1.1-0.tar.gz
TipDatingBeast_1.1-0.zip(r-4.7)TipDatingBeast_1.1-0.zip(r-4.6)TipDatingBeast_1.1-0.zip(r-4.5)
TipDatingBeast_1.1-0.tgz(r-4.6-any)TipDatingBeast_1.1-0.tgz(r-4.5-any)
TipDatingBeast_1.1-0.tar.gz(r-4.7-any)TipDatingBeast_1.1-0.tar.gz(r-4.6-any)
TipDatingBeast_1.1-0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TipDatingBeast/json (API)
| # Install 'TipDatingBeast' in R: |
| install.packages('TipDatingBeast', repos = c('https://ckhatchikian.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:b23bcc57c3. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 141 | ||
| source / vignettes | OK | 194 | ||
| linux-release-x86_64 | OK | 147 | ||
| macos-release-arm64 | OK | 165 | ||
| macos-oldrel-arm64 | OK | 184 | ||
| windows-devel | OK | 94 | ||
| windows-release | OK | 95 | ||
| windows-oldrel | OK | 105 | ||
| wasm-release | OK | 121 |
Exports:ListTaxaPlotDRTPlotLOOCVRandomClusterRandomDatesTaxaOutTaxonOut
Dependencies:askpassbitbit64bootcellrangerclassclicliprcpp11crayoncurldata.tableDescToolse1071ExactexpmforcatsfsgldgluehavenhmshttrjsonlitelatticelifecyclelmommagrittrMASSMatrixmclustmimemvtnormopensslpillarpkgconfigprettyunitsprogressproxyR6RcppreadrreadxlrematchrlangrootSolverstudioapisysTeachingDemostibbletidyselecttzdbutf8vctrsvroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Tip dating of phylogenetic trees with BEAST | TipDatingBeast-package TipDatingBeast |
| List taxa names present in the BEAST input file | LISTTAXA ListTaxa |
| List taxa names present in the BEAST input file | PLOTDRT PlotDRT |
| List taxa names present in the BEAST input file | PLOTLOOCV PlotLOOCV |
| randomize dates among tips in the BEAST input file | RANDOMCLUSTER RandomCluster |
| randomize dates among tips in the BEAST input file | RANDOMDATES RandomDates |
| generates input files for leave-one-out analyses in BEAST | TAXAOUT TaxaOut |
| single Taxon out input file for leave-one-out analysis in BEAST | TAXONOUT TaxonOut |
