Package: paleotree 3.4.7
paleotree: Paleontological and Phylogenetic Analyses of Evolution
Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.
Authors:
paleotree_3.4.7.tar.gz
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paleotree_3.4.7.tgz(r-4.4-any)paleotree_3.4.7.tgz(r-4.3-any)
paleotree_3.4.7.tar.gz(r-4.5-noble)paleotree_3.4.7.tar.gz(r-4.4-noble)
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paleotree.pdf |paleotree.html✨
paleotree/json (API)
# Install 'paleotree' in R: |
install.packages('paleotree', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dwbapst/paleotree/issues
- ammoniteTraitsRaia - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
- ammoniteTreeRaia - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
- ceratopsianTreeRaia - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
- cervidTreeRaia - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
- charMatDicrano - Cladistic Data for Dicranograptid Graptolites from Song and Zhang
- cladogramDicranoX12 - Cladistic Data for Dicranograptid Graptolites from Song and Zhang
- cladogramDicranoX13 - Cladistic Data for Dicranograptid Graptolites from Song and Zhang
- foramAL - Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al.
- foramALb - Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al.
- foramAM - Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al.
- foramAMb - Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al.
- graptCharMatrix - Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
- graptDistMat - Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
- graptOccPBDB - Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
- graptRanges - Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
- graptTaxaPBDB - Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
- graptTimeTree - Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
- graptTree - Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
- kanto - Example Species Abundances Tables
- retioChar - Cladogram and Range Data for the Retiolitinae
- retioRanges - Cladogram and Range Data for the Retiolitinae
- retioTree - Cladogram and Range Data for the Retiolitinae
- shellSize - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
- sutureComplexity - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
Last updated 2 months agofrom:72ad91ba4c. Checks:OK: 1 NOTE: 6. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 07 2024 |
R-4.5-win | NOTE | Sep 07 2024 |
R-4.5-linux | NOTE | Sep 07 2024 |
R-4.4-win | NOTE | Sep 07 2024 |
R-4.4-mac | NOTE | Sep 07 2024 |
R-4.3-win | NOTE | Sep 07 2024 |
R-4.3-mac | NOTE | Sep 07 2024 |
Exports:accioBestAcquisitionModelaccioExhaustionCurveaddTermBranchLengthancPropStateMatbin_cal3TimePaleoPhybin_timePaleoPhybindPaleoTipbinTimeDatabranchClassescal3TimePaleoPhycharExhaustPlotcladogeneticTraitContcleanNewPhylocollapseNodescompareNodeAgescompareTermBranchesconstrainParPaleocreateMrBayesConstraintscreateMrBayesTipCalibrationscreateMrBayesTipDatingNexusdateNodesdateTaxonTreePBDBdeadTreedegradeTreedepthRainbowdivCurveFossilRecordSimdropExtantdropExtinctdropPaleoTipdropZLBequation2functionexpandTaxonTreefixRootTimefooteValuesfossilRecord2fossilRangesfossilRecord2fossilTaxafossilTaxa2fossilRecordfourDate2timeListfreqRatgetCladeTaxaPBDBgetPBDBoccgetSpecificTaxaPBDBhorizonSampRateHurlbertPIEmake_durationFreqContmake_durationFreqDiscmake_inverseSurvmakePBDBtaxonTreeminBranchLengthminCharChangemultiDivnearestNeighborDistnodeDates2branchLengthsobtainDatedPosteriorTreesMrBoccData2timeListoptimPaleopairwiseSpearmanRhoparboundsparbounds<-parentChild2taxonTreeparInitparLowerparLower<-parnamesparnames<-parUpperparUpper<-perCapitaRatesperfectParsCharTreephyloDivplotMultiDivplotOccDataplotPhyloPicTreeplotTaxaTreePBDBplotTraitgrampqr2PspqsRate2sProbprobAncqsProb2CompqsRate2CompresolveTreeCharreverseListrootSplitsampleRangesseqTimeListsetRootAgesetRootAgessimFossilRecordsimTermTaxasimTermTaxaAdvancedsProb2sRatesRate2sProbtaxa2cladogramtaxa2phylotaxicDivConttaxicDivDisctaxonSortPBDBocctaxonTable2taxonTreetestEdgeMattimeLadderTreetimeList2fourDatetimePaleoPhytimeSliceFossilRecordtimeSliceTreetipDatingCompatabilitySummaryMrBtreeContradictiontrueTermTaxaTreetwoWayEcologyClusterunitLengthTree
Dependencies:apebitopscliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdigestdoParallelexpmfansifarverfastmatchforeachgenericsggplot2ggseqlogogluegtableigraphisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellnlmenumDerivoptimParallelphangornphytoolspillarpkgconfigpngquadprogR6RColorBrewerRcppRCurlrlangscalesscatterplot3dtibbleutf8vctrsviridisLitewithr