Package: BoskR 1.1.2
Orlando Schwery
BoskR: Assess Adequacy of Diversification Models Using Tree Shapes
Given a phylogeny (or several) and a diversification model (or several), the package makes use of graph Laplacians (as implemented in RPANDA) and other tree shape metrics to infer summary statistics. The overlap of those metrics will be compared to the metrics from a set of trees simulated under the model in question and based on the same parameters as the initial tree. If the metrics indicate that the shapes of the simulated trees significantly differ from the initial one, the model should be deemed not adequate for this tree.
Authors:
BoskR_1.1.2.tar.gz
BoskR_1.1.2.zip(r-4.5)BoskR_1.1.2.zip(r-4.4)BoskR_1.1.2.zip(r-4.3)
BoskR_1.1.2.tgz(r-4.4-any)BoskR_1.1.2.tgz(r-4.3-any)
BoskR_1.1.2.tar.gz(r-4.5-noble)BoskR_1.1.2.tar.gz(r-4.4-noble)
BoskR_1.1.2.tgz(r-4.4-emscripten)BoskR_1.1.2.tgz(r-4.3-emscripten)
BoskR.pdf |BoskR.html✨
BoskR/json (API)
| # Install 'BoskR' in R: |
| install.packages('BoskR', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/oschwery/boskr/issues
- emptesttrees - Set of Test Trees for BoskR
Last updated 7 months agofrom:47659baea5. Checks:ERROR: 1 WARNING: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 29 2024 |
| R-4.5-win | WARNING | Oct 29 2024 |
| R-4.5-linux | WARNING | Oct 29 2024 |
| R-4.4-win | WARNING | Oct 29 2024 |
| R-4.4-mac | WARNING | Oct 29 2024 |
| R-4.3-win | WARNING | Oct 29 2024 |
| R-4.3-mac | WARNING | Oct 29 2024 |
Exports:CombineTreesGetMetricTreeSetsGetTreeMetricsGetTreeParamsplotPvalMetricsCDFplotPvalMetricsPDFPvalMetricsScatterMetricsTreeCorr
Dependencies:abindade4apeaskpassbackportsBBBHbipartitebootbroomcarcarDataclasscliclueclusterclusterGenerationcodacodetoolscolorspacecombinatcorpcorcowplotcpp11crayoncurlDDDDEoptimDEoptimRDerivdeSolvedigestdiptestdirmultdiversitreedoBydoParalleldotCall64dplyrexpmfansifarverfBasicsfieldsflexmixforeachFormulafpcgeigergenericsggplot2ggrepelglassoFastgluegmpgssgtableGUniFrachmshttrigraphinlineisobanditeratorsjsonlitekernlablabelinglatticelifecyclelme4magrittrmapsMASSMatrixMatrixModelsmatrixStatsmclustmgcvmicrobenchmarkmimeminqamnormtmodeestmodelrmodeltoolsmunsellmvMORPHmvtnormncbitnetworkNHPoissonnlmenloptrnnetnumDerivopenssloptimParallelParallelLoggerpbkrtestpbmcapplypermutephangornphylobasephyloTopphytoolspicantepillarpixmappkgconfigplyrprabcluspracmaprettyunitsprogresspsplinepurrrpvclustquadprogquantregR.methodsS3R.ooR.utilsR6rasterRColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangRmpfrrmutilrnclRNeXMLrobustbaseRPANDArpartscalesscatterplot3dsnasnowspspamSparseMspatialstablestablediststatipstatmodstatnet.commonstringistringrsubplexsurvivalsysterraTESStibbletidyrtidyselecttimeDatetimeSeriesTreeSimutf8uuidvctrsveganviridisLitewithrXMLxml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BoskR - Assess Adequacy of Diversification Models Using Tree Shapes | BoskR-package BoskR |
| Rearrange Input Trees | CombineTrees |
| Set of Test Trees for BoskR | emptesttrees |
| Simulate trees based on empirical estimations or set parameters | GetMetricTreeSets |
| Get metrics describing tree shape | GetTreeMetrics |
| Get diversification parameters from trees | GetTreeParams |
| Plot p-values on CDF for sets of tree metrics | plotPvalMetricsCDF |
| Plot p-values on PDF for sets of tree metrics | plotPvalMetricsPDF |
| Get p-values for tree metrics | PvalMetrics |
| 3D Metrics Scatterplot | ScatterMetrics |
| Run Tests and Corrections for Trees | TreeCorr |
