Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 1997)
Sorting Unique Taxa of a Given Rank from Paleobiology Database Occurrence Data
Miscellaneous Functions for Community Ecology
Simulate Cladogenetic Trait Evolution
Convert Simulated Taxon Data into a Phylogeny
Calculates Values for Foote's Inverse Survivorship Analyses
Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges
Time-Slicing a Phylogeny
Converting Sampling Estimates
Bin Simulated Temporal Ranges in Discrete Intervals
Example Species Abundances Tables
Inverse Survivorship Models in the Fossil Record
Model Function Methods: Parameter Names, Bounds and Initial Values
Creating a Taxon-Tree from Taxonomic Data Downloaded from the Paleobiology Database
Convert Simulated Taxon Data into a Cladogram
Reverse List Structure
Converting Datasets of Taxon Ranges in Intervals Between timeList format and fourDate format
Scale Tree to Unit-Length
Estimating the Minimum Number of Character Transitions Using Maximum Parsimony
Absolute Dates for Nodes of a Time-Scaled Phylogeny
Models of Sampling and Extinction for Taxonomic Duration Datasets
Nearest Neighbor Distances for Morphological Disparity Studies
Joint Probability of A Clade Surviving Infinitely or Being Sampled Once
Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
Simplified Optimizer for paleotree Likelihood Functions
Diversity-Curve Plotting for Simulations of Diversification and Sampling In the Fossil Record
Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
Simulating Un-Conditioned Trees of Fossil Taxa
Simulating Extinct Clades of Monophyletic Taxa
Extrapolating Lower-Level Taxon Phylogenies from Higher-Level Taxon Trees
Constrain Parameters for a Model Function from paleotree
Construct a Stochastic Sequenced Time-List from an Unsequenced Time-List
Sampling Taxon Ranges
Paint Tree Branch Depth by Color
Transform a Topology into a Set of Constraint Commands for MrBayes
paleotree: Paleontological and Phylogenetic Analyses of Evolution
Turn a Character String of the Right-Hand Side of an Equation into an R Function
Timescaling of Paleo-Phylogenies
Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Hierarchical Table of Taxonomy Memberships
Cladogram and Range Data for the Retiolitinae
Plotting Occurrence Data Across Taxa
Randomly Collapse a Portion of Nodes on a Phylogeny
Converting Occurrences Data to a timeList Data Object
Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table of Parent-Child Taxon Relationships
Probability of being a sampled ancestor of another sampled taxon
Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
Fit Models of Sampling Rates to Continuous-Time Taxon Ranges
Simulating Taxa in the Fossil Record
perCapitaRates
Split Tip Taxa by Root Divergence
Methods for Editing or Converting Output from simFossilRecord
Simulate a Set of Parsimony-Informative Characters for a Phylogeny
Partitions the branch lengths of a tree into several classes based on their placement.
Three Rate Calibrated Timescaling of Paleo-Phylogenies
Comparing the Time-Scaling of Trees
Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
Full-Scale Simulations of the Fossil Record with Birth, Death and Sampling of Morphotaxa
Frequency Ratio Method for Estimating Sampling Probability
Diversity Curves
Resolve Polytomies Using Parsimony-Based Reconstruction of a Discrete Character
Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
Resolve Polytomies by Order of First Appearance
Simulating Taxa in the Fossil Record, Conditioned on Sampling Rate
Plot a Traitgram for Continuous Traits
Calculating Diversity Curves Across Multiple Datasets
Test the Edge Matrix of a 'phylo' Phylogeny Object for Inconsistencies