Paleontological and Phylogenetic Analyses of Evolution
Bin Simulated Temporal Ranges in Discrete Intervals
Partitions the branch lengths of a tree into several classes based on ...
Three Rate Calibrated a posteriori Dating of Paleontological Phylo...
Simulate Cladogenetic Trait Evolution
Miscellaneous Functions for Community Ecology
Comparing the Time-Scaling of Trees
Constrain Parameters for a Model Function from paleotree
Transform a Topology into a Set of Constraint Commands for MrBayes
Construct A Block of Tip Age Calibrations for Use with Tip-Dating Anal...
Construct a Fully Formatted NEXUS Script for Performing Tip-Dating Ana...
Absolute Dates for Nodes of a Time-Scaled Phylogeny
Date a Taxon-Topology from the Paleobiology Database Using Appearance ...
Randomly Collapse a Portion of Nodes on a Phylogeny
Paint Tree Branch Depth by Color
Diversity-Curve Plotting for Simulations of Diversification and Sampli...
Diversity Curves
Models of Sampling and Extinction for Taxonomic Duration Datasets
Turn a Character String of the Right-Hand Side of an Equation into an ...
Analyses of the exhaustion of Character States Over Evolutionary Histo...
Extrapolating Lower-Level Taxon Phylogenies from Higher-Level Taxon Tr...
Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Pa...
Calculates Values for Foote's Inverse Survivorship Analyses
Frequency Ratio Method for Estimating Sampling Probability
Obtaining Data for Taxa or Occurrences From Paleobiology Database API
Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 19...
Inverse Survivorship Models in the Fossil Record
Creating a Taxon-Tree from Taxonomic Data Downloaded from the Paleobio...
Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
Estimating the Minimum Number of Character Transitions Using Maximum P...
Model Function Methods: Parameter Names, Bounds and Initial Values
Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Pa...
Calculating Diversity Curves Across Multiple Datasets
Nearest Neighbor Distances for Morphological Disparity Studies
Obtaining Edge Lengths for Undated Phylogenies Using Known Branching N...
Get the Sample of Posterior Trees from a Dated Phylogenetic Analysis w...
Converting Occurrences Data to a timeList Data Object
Simplified Optimizer for paleotree Likelihood Functions
paleotree: Paleontological and Phylogenetic Analyses of Evolution
Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table of Paren...
Instantaneous per-Capita Rates of Origination and Extinction from ...
Simulate a Set of Parsimony-Informative Characters for a Phylogeny
Plotting Occurrence Data Across Taxa
Plot a Phylogeny with Organismal Silhouettes from PhyloPic, Called Via...
Plot a Traitgram for Continuous Traits
Joint Probability of A Clade Surviving Infinitely or Being Sampled Onc...
Probability of being a sampled ancestor of another sampled taxon
Resolve Polytomies Using Parsimony-Based Reconstruction of a Discrete ...
Reverse List Structure
Split Tip Taxa by Root Divergence
Sampling Taxon Ranges
Converting Sampling Estimates
Construct a Stochastic Sequenced Time-List from an Unsequenced Time-Li...
Place a Non-Ultrametric Tree of Fossil Taxa on Absolute Time
Full-Scale Simulations of the Fossil Record with Birth, Death and Samp...
Methods for Editing or Converting Output from Simulated Fossil Record ...
Convert Simulated Taxon Data into a Cladogram
Convert Simulated Taxon Data into a Phylogeny
Sorting Unique Taxa of a Given Rank from Paleobiology Database Occurre...
Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Hierarchical T...
Simulating Extinct Clades of Monophyletic Taxa
Test the Edge Matrix of a 'phylo' Phylogeny Object for Inconsistenci...
Resolve Polytomies by Order of First Appearance
Converting Datasets of Taxon Ranges in Intervals Between timeList fo...
Simplistic a posteriori Dating Approaches For Paleontological Phyl...
Time-Slicing a Phylogeny
Get the Compatibility Summary Topology From a Tip-Dating Analysis with...
Measure the Contradiction Difference Between Two Phylogenetic Topologi...
R-Mode vs Q-Mode Two-Way Cluster Analyses and Abundance Plot for Commu...
Scale Tree to Unit-Length
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.