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paleotree (version 2.5)

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.

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Install

install.packages('paleotree')

Monthly Downloads

841

Version

2.5

License

CC0

Issues

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Repository

https://github.com/dwbapst/paleotree

Homepage

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

Maintainer

David Bapst

Last Published

September 21st, 2015

Functions in paleotree (2.5)

horizonSampRate

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

taxonSortPBDBocc

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

communityEcology

Miscellaneous Functions for Community Ecology

cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution

Convert Simulated Taxon Data into a Phylogeny

Calculates Values for Foote's Inverse Survivorship Analyses

getSampProbDisc

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

makePBDBtaxonTree

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

Convert Simulated Taxon Data into a Cladogram

Reverse List Structure

timeList2fourDate

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

nearestNeighborDist

Nearest Neighbor Distances for Morphological Disparity Studies

Joint Probability of A Clade Surviving Infinitely or Being Sampled Once

minBranchLength

Scales Edge Lengths of a Phylogeny to a Minimum Branch Length

macroperforateForam

Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)

Simplified Optimizer for paleotree Likelihood Functions

divCurveFossilRecordSim

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

expandTaxonTree

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

constrainParPaleo

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

createMrBayesConstraints

Transform a Topology into a Set of Constraint Commands for MrBayes

paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution

equation2function

Turn a Character String of the Right-Hand Side of an Equation into an R Function

Timescaling of Paleo-Phylogenies

taxonTable2taxonTree

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

occData2timeList

Converting Occurrences Data to a timeList Data Object

parentChild2taxonTree

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

modifyTerminalBranches

Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)

getSampRateCont

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges

Simulating Taxa in the Fossil Record

Split Tip Taxa by Root Divergence

simFossilRecordMethods

Methods for Editing or Converting Output from simFossilRecord

perfectParsCharTree

Simulate a Set of Parsimony-Informative Characters for a Phylogeny

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

cal3TimePaleoPhy

Three Rate Calibrated Timescaling of Paleo-Phylogenies

compareTimescaling

Comparing the Time-Scaling of Trees

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

simFossilRecord

Full-Scale Simulations of the Fossil Record with Birth, Death and Sampling of Morphotaxa

Frequency Ratio Method for Estimating Sampling Probability

DiversityCurves

Diversity Curves

resolveTreeChar

Resolve Polytomies Using Parsimony-Based Reconstruction of a Discrete Character

SongZhangDicrano

Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)

Resolve Polytomies by Order of First Appearance

simFossilTaxa_SRCond

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