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:Orlando Schwery [aut, cre]

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# 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

Datasets:

On CRAN:

Conda:

2.00 score 1 stars 2 scripts 9 exports 175 dependencies

Last updated 10 months agofrom:47659baea5. Checks:1 ERROR, 7 WARNING. Indexed: no.

TargetResultLatest binary
Doc / VignettesFAILFeb 26 2025
R-4.5-winWARNINGFeb 26 2025
R-4.5-macWARNINGFeb 26 2025
R-4.5-linuxWARNINGFeb 26 2025
R-4.4-winWARNINGFeb 26 2025
R-4.4-macWARNINGFeb 26 2025
R-4.3-winWARNINGFeb 26 2025
R-4.3-macWARNINGFeb 26 2025

Exports:CombineTreesGetMetricTreeSetsGetTreeMetricsGetTreeParamsplotPvalMetricsCDFplotPvalMetricsPDFPvalMetricsScatterMetricsTreeCorr

Dependencies:abindade4apeaskpassbackportsBBBHbipartitebootbroomcarcarDatacheckmateclasscliclueclusterclusterGenerationcodacodetoolscolorspacecombinatcorpcorcowplotcpp11crayoncurlDDDDEoptimDEoptimRDerivdeSolvedigestdiptestdirmultdiversitreedoBydoParalleldotCall64dplyrexpmfansifarverfBasicsfieldsflexmixforeachFormulafpcgeigergenericsggplot2ggrepelglassoFastgluegmpgssgtableGUniFrachmshttrigraphinlineisobanditeratorsjsonlitekernlablabelinglatticelifecyclelme4magrittrmapsMASSMatrixMatrixModelsmatrixStatsmclustmgcvmicrobenchmarkmimeminqamnormtmodeestmodelrmodeltoolsmunsellmvMORPHmvtnormncbitnetworkNHPoissonnlmenloptrnnetnumDerivopenssloptimParallelParallelLoggerpbkrtestpbmcapplypermutephangornphylobasephyloTopphytoolspicantepillarpixmappkgconfigplyrprabcluspracmaprettyunitsprogresspsplinepurrrpvclustquadprogquantregR.methodsS3R.ooR.utilsR6rasterrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangRmpfrrmutilrnclRNeXMLrobustbaseRPANDArpartscalesscatterplot3dsnasnowspspamSparseMspatialstablestablediststatipstatmodstatnet.commonstringistringrsubplexsurvivalsysterraTESStibbletidyrtidyselecttimeDatetimeSeriesTreeSimutf8uuidvctrsveganviridisLitewithrXMLxml2