Man pages for dwbapst/paleotree
Paleontological and Phylogenetic Analyses of Evolution
| binTimeData | Bin Simulated Temporal Ranges in Discrete Intervals |
| branchClasses | Partitions the branch lengths of a tree into several classes... |
| cal3TimePaleoPhy | Three Rate Calibrated _a posteriori_ Dating of... |
| cladogeneticTraitCont | Simulate Cladogenetic Trait Evolution |
| communityEcology | Miscellaneous Functions for Community Ecology |
| compareTimescaling | Comparing the Time-Scaling of Trees |
| constrainParPaleo | Constrain Parameters for a Model Function from paleotree |
| createMrBayesConstraints | Transform a Topology into a Set of Constraint Commands for... |
| createMrBayesTipCalibrations | Construct A Block of Tip Age Calibrations for Use with... |
| createMrBayesTipDatingNexus | Construct a Fully Formatted NEXUS Script for Performing... |
| dateNodes | Absolute Dates for Nodes of a Time-Scaled Phylogeny |
| dateTaxonTreePBDB | Date a Taxon-Topology from the Paleobiology Database Using... |
| degradeTree | Randomly Collapse a Portion of Nodes on a Phylogeny |
| depthRainbow | Paint Tree Branch Depth by Color |
| divCurveFossilRecordSim | Diversity-Curve Plotting for Simulations of Diversification... |
| DiversityCurves | Diversity Curves |
| durationFreq | Models of Sampling and Extinction for Taxonomic Duration... |
| equation2function | Turn a Character String of the Right-Hand Side of an Equation... |
| exhaustionFunctions | Analyses of the exhaustion of Character States Over... |
| expandTaxonTree | Extrapolating Lower-Level Taxon Phylogenies from Higher-Level... |
| fixRootTime | Modify, Drop or Bind Terminal Branches of Various Types... |
| footeValues | Calculates Values for Foote's Inverse Survivorship Analyses |
| freqRat | Frequency Ratio Method for Estimating Sampling Probability |
| getDataPBDB | Obtaining Data for Taxa or Occurrences From Paleobiology... |
| graptDisparity | Morphlogical Character and Range Data for late Ordovician and... |
| graptPBDB | Example Occurrence and Taxonomic Datasets of the... |
| horizonSampRate | Estimate Sampling Rate from Sampling Horizon Data (Solow and... |
| inverseSurv | Inverse Survivorship Models in the Fossil Record |
| kanto | Example Species Abundances Tables |
| macroperforateForam | Ancestor-Descendant Relationships for Macroperforate... |
| makePBDBtaxonTree | Creating a Taxon-Tree from Taxonomic Data Downloaded from the... |
| minBranchLength | Scales Edge Lengths of a Phylogeny to a Minimum Branch Length |
| minCharChange | Estimating the Minimum Number of Character Transitions Using... |
| modelMethods | Model Function Methods: Parameter Names, Bounds and Initial... |
| modifyTerminalBranches | Modify, Drop or Bind Terminal Branches of Various Types... |
| multiDiv | Calculating Diversity Curves Across Multiple Datasets |
| nearestNeighborDist | Nearest Neighbor Distances for Morphological Disparity... |
| nodeDates2branchLengths | Obtaining Edge Lengths for Undated Phylogenies Using Known... |
| obtainDatedPosteriorTreesMrB | Get the Sample of Posterior Trees from a Dated Phylogenetic... |
| occData2timeList | Converting Occurrences Data to a 'timeList' Data Object |
| optimPaleo | Simplified Optimizer for 'paleotree' Likelihood Functions |
| paleotree-package | paleotree: Paleontological and Phylogenetic Analyses of... |
| parentChild2taxonTree | Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table... |
| perCapitaRates | Instantaneous _per-Capita_ Rates of Origination and... |
| perfectParsCharTree | Simulate a Set of Parsimony-Informative Characters for a... |
| plotOccData | Plotting Occurrence Data Across Taxa |
| plotPhyloPicTree | Plot a Phylogeny with Organismal Silhouettes from PhyloPic,... |
| plotTraitgram | Plot a Traitgram for Continuous Traits |
| pqr2Ps | Joint Probability of A Clade Surviving Infinitely or Being... |
| probAnc | Probability of being a sampled ancestor of another sampled... |
| RaiaCopesRule | Dated Trees and Trait Data for Ammonites, Ceratopsians and... |
| resolveTreeChar | Resolve Polytomies Using Parsimony-Based Reconstruction of a... |
| retiolitinae | Cladogram and Range Data for the Retiolitinae |
| reverseList | Reverse List Structure |
| rootSplit | Split Tip Taxa by Root Divergence |
| sampleRanges | Sampling Taxon Ranges |
| SamplingConv | Converting Sampling Estimates |
| seqTimeList | Construct a Stochastic Sequenced Time-List from an... |
| setRootAge | Place a Non-Ultrametric Tree of Fossil Taxa on Absolute Time |
| simFossilRecord | Full-Scale Simulations of the Fossil Record with Birth, Death... |
| simFossilRecordMethods | Methods for Editing or Converting Output from Simulated... |
| SongZhangDicrano | Cladistic Data for Dicranograptid Graptolites from Song and... |
| taxa2cladogram | Convert Simulated Taxon Data into a Cladogram |
| taxa2phylo | Convert Simulated Taxon Data into a Phylogeny |
| taxonSortPBDBocc | Sorting Unique Taxa of a Given Rank from Paleobiology... |
| taxonTable2taxonTree | Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a... |
| termTaxa | Simulating Extinct Clades of Monophyletic Taxa |
| testEdgeMat | Test the Edge Matrix of a "phylo" Phylogeny Object for... |
| timeLadderTree | Resolve Polytomies by Order of First Appearance |
| timeList2fourDate | Converting Datasets of Taxon Ranges in Intervals Between... |
| timePaleoPhy | Simplistic _a posteriori_ Dating Approaches For... |
| timeSliceTree | Time-Slicing a Phylogeny |
| tipDatingCompatabilitySummaryMrB | Get the Compatibility Summary Topology From a Tip-Dating... |
| treeContradiction | Measure the Contradiction Difference Between Two Phylogenetic... |
| twoWayEcologyCluster | R-Mode vs Q-Mode Two-Way Cluster Analyses and Abundance Plot... |
| unitLengthTree | Scale Tree to Unit-Length |
