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Package 'Paleotree' Package ‘paleotree’ December 12, 2019 Type Package Version 3.3.25 Title Paleontological and Phylogenetic Analyses of Evolution Date 2019-12-12 Author David W. Bapst, Peter J. Wagner Depends R (>= 3.0.0), ape (>= 4.1) Imports phangorn (>= 2.0.0), stats, phytools (>= 0.6-00), jsonlite, graphics, grDevices, methods, png, RCurl, utils Suggests spelling, testthat Language en-US ByteCompile TRUE Encoding UTF-8 Maintainer David W. Bapst <[email protected]> BugReports https://github.com/dwbapst/paleotree/issues Description 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. 1 2 R topics documented: License CC0 URL https://github.com/dwbapst/paleotree RoxygenNote 7.0.2 NeedsCompilation no Repository CRAN Date/Publication 2019-12-12 12:50:02 UTC R topics documented: paleotree-package . .4 binTimeData . .6 branchClasses . .8 cal3TimePaleoPhy . 10 cladogeneticTraitCont . 23 communityEcology . 25 compareTimescaling . 28 constrainParPaleo . 30 createMrBayesConstraints . 35 createMrBayesTipCalibrations . 36 createMrBayesTipDatingNexus . 40 dateNodes . 48 dateTaxonTreePBDB . 50 degradeTree . 54 depthRainbow . 56 divCurveFossilRecordSim . 57 DiversityCurves . 58 durationFreq . 63 equation2function . 67 exhaustionFunctions . 69 expandTaxonTree . 72 fixRootTime . 74 footeValues . 76 freqRat . 78 getDataPBDB . 84 graptDisparity . 87 graptPBDB . 91 horizonSampRate . 94 inverseSurv . 96 kanto . 101 macroperforateForam . 106 makePBDBtaxonTree . 113 minBranchLength . 118 minCharChange . 120 modelMethods . 128 modifyTerminalBranches . 132 multiDiv . 138 R topics documented: 3 nearestNeighborDist . 143 nodeDates2branchLengths . 144 obtainDatedPosteriorTreesMrB . 147 occData2timeList . 151 optimPaleo . 154 parentChild2taxonTree . 155 perCapitaRates . 157 perfectParsCharTree . 160 plotOccData . 162 plotPhyloPicTree . 163 plotTraitgram . 170 pqr2Ps . 172 probAnc . 174 RaiaCopesRule . 176 resolveTreeChar . 181 retiolitinae . 186 reverseList . 188 rootSplit . 189 sampleRanges . 189 SamplingConv . 195 seqTimeList . 197 setRootAge . 200 simFossilRecord . 201 simFossilRecordMethods . 224 SongZhangDicrano . 228 taxa2cladogram . 230 taxa2phylo . 232 taxonSortPBDBocc . 234 taxonTable2taxonTree . 238 termTaxa . 239 testEdgeMat . 244 timeLadderTree . 246 timeList2fourDate . 247 timePaleoPhy . 249 timeSliceTree . 262 tipDatingCompatabilitySummaryMrB . 265 treeContradiction . 268 twoWayEcologyCluster . 271 unitLengthTree . 274 Index 276 4 paleotree-package paleotree-package paleotree: Paleontological and Phylogenetic Analyses of Evolution Description Analyzes, time-scales and simulates phylogenies of extinct/fossil lineages, along with calculation of diversity curves. Also fits likelihood models to estimate sampling rates from stratigraphic ranges. Details Package: paleotree Type: Package License: CC0 This package contains functions for analyzing sampling rates given ranges of fossil taxa, in both continuous and discrete time, functions for a posteriori time-scaling phylogenies of fossil taxa and functions for simulating the fossil record in both taxic and phylogenetic varieties. Author(s) David W. Bapst Maintainer: David W. Bapst <[email protected]> References Bapst, D.W. 2012. paleotree: an R package for paleontological and phylogenetic analyses of evo- lution. Methods in Ecology and Evolution. 3: 803-807. doi: 10.1111/j.2041-210X.2012.00223.x Bapst, D. W. 2013. A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa. Methods in Ecology and Evolution. 4(8):724-733. Bapst, D. W. 2013. When Can Clades Be Potentially Resolved with Morphology? PLoS ONE. 8(4):e62312. Bapst, D. W. 2014. Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record. Paleobiology 40(3):331-351. See Also This package relies extensively on the phylogenetic toolkit and standards offered by the ape pack- age, and hence lists this package as a depends, so it is loaded simultaneously. Examples # get the package version of paleotree packageVersion("paleotree") paleotree-package 5 # get the citation for paleotree citation("paleotree") ## Simulate some fossil ranges with simFossilRecord set.seed(444); record <- simFossilRecord( p = 0.1, q = 0.1, nruns = 1, nTotalTaxa = c(30,40), nExtant = 0 ) taxa <- fossilRecord2fossilTaxa(record) # let's see what the 'true' diversity curve looks like in this case # plot the FADs and LADs.
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