Learn R Programming

⚠️There's a newer version (3.4.7) of this package.Take me there.

paleotree (version 2.4)

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.

Copy Link

Version

Install

install.packages('paleotree')

Monthly Downloads

980

Version

2.4

License

CC0

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/dwbapst/paleotree

Homepage

http://webpages.sdsmt.edu/~dbapst/

Maintainer

David Bapst

Last Published

May 2nd, 2015

Functions in paleotree (2.4)

Inverse Survivorship Models in the Fossil Record

occData2timeList

Converting Occurrences Data to a timeList Data Object

Convert Simulated Taxon Data into a Cladogram

Simulating Taxa in the Fossil Record

Test the Edge Matrix of a 'phylo' Phylogeny Object for Inconsistencies

DiversityCurves

Diversity Curves

Probability of being a sampled ancestor of another sampled taxon

Converting Sampling Estimates

Models of Sampling and Extinction for Taxonomic Duration Datasets

expandTaxonTree

Extrapolating Lower-Level Taxon Phylogenies from Higher-Level Taxon Trees

cal3TimePaleoPhy

Three Rate Calibrated Timescaling of Paleo-Phylogenies

Bin Simulated Temporal Ranges in Discrete Intervals

perfectParsCharTree

Simulate a Set of Parsimony-Informative Characters for a Phylogeny

Model Function Methods: Parameter Names, Bounds and Initial Values

Plotting Occurrence Data Across Taxa

Plot a Traitgram for Continuous Traits

Paint Tree Branch Depth by Color

Time-Slicing a Phylogeny

Calculates Values for Foote's Inverse Survivorship Analyses

minBranchLength

Scales Edge Lengths of a Phylogeny to a Minimum Branch Length

getSampRateCont

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges

Simulating Un-Conditioned Trees of Fossil Taxa

Split Tip Taxa by Root Divergence

nearestNeighborDist

Nearest Neighbor Distances for Morphological Disparity Studies

Timescaling of Paleo-Phylogenies

Scale Tree to Unit-Length

taxonTable2taxonTree

Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Hierarchical Table of Taxonomy Memberships

constrainParPaleo

Constrain Parameters for a Model Function from paleotree

simFossilTaxa_SRCond

Simulating Taxa in the Fossil Record, Conditioned on Sampling Rate

Resolve Polytomies by Order of First Appearance

Cladogram and Range Data for the Retiolitinae

Randomly Collapse a Portion of Nodes on a Phylogeny

Frequency Ratio Method for Estimating Sampling Probability

resolveTreeChar

Resolve Polytomies Using Parsimony-Based Reconstruction of a Discrete Character

Calculating Diversity Curves Across Multiple Datasets

Convert Simulated Taxon Data into a Phylogeny

Simulating Extinct Clades of Monophyletic Taxa

Construct a Stochastic Sequenced Time-List from an Unsequenced Time-List

timeList2fourDate

Converting Datasets of Taxon Ranges in Intervals Between timeList format and fourDate format

Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea

getSampProbDisc

Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges

Estimating the Minimum Number of Character Transitions Using Maximum Parsimony

cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution

Joint Probability of A Clade Surviving Infinitely or Being Sampled Once

taxonSortPBDBocc

Sorting Unique Taxa of a Given Rank from Paleobiology Database Occurrence Data

compareTimescaling

Comparing the Time-Scaling of Trees

horizonSampRate

Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 1997)

Reverse List Structure

parentChild2taxonTree

Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table of Parent-Child Taxon Relationships

makePBDBtaxonTree

Creating a Taxon-Tree from Taxonomic Data Downloaded from the Paleobiology Database

Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database

Simplified Optimizer for paleotree Likelihood Functions

Sampling Taxon Ranges

Partitions the branch lengths of a tree into several classes based on their placement.

Absolute Dates for Nodes of a Time-Scaled Phylogeny

modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types

paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution