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

paleotree (version 2.2)

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

736

Version

2.2

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

September 18th, 2014

Functions in paleotree (2.2)

getSampRateCont

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges
cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution
simFossilTaxa_SRCond

Simulating Taxa in the Fossil Record, Conditioned on Sampling Rate
perfectParsCharTree

Simulate a Set of Parsimony-Informative Characters for a Phylogeny
retiolitinae

Cladogram and Range Data for the Retiolitinae
depthRainbow

Paint Tree Branch Depth by Color
termTaxa

Simulating Extinct Clades of Monophyletic Taxa
modelMethods

Model Function Methods: Parameter Names, Bounds and Initial Values
optimPaleo

Simplified Optimizer for paleotree Likelihood Functions
pqr2Ps

Joint Probability of A Clade Surviving Infinitely or Being Sampled Once
cal3TimePaleoPhy

Three Rate Calibrated Timescaling of Paleo-Phylogenies
expandTaxonTree

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

Randomly Collapse a Portion of Nodes on a Phylogeny
unitLengthTree

Scale Tree to Unit-Length
timeSliceTree

Time-Slicing a Phylogeny
constrainParPaleo

Constrain Parameters for a Model Function from paleotree
modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types
freqRat

Frequency Ratio Method for Estimating Sampling Probability
DiversityCurves

Diversity Curves
branchClasses

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

Plot a Traitgram for Continuous Traits
taxa2cladogram

Convert Simulated Taxon Data into a Cladogram
rootSplit

Split Tip Taxa by Root Divergence
footeValues

Calculates Values for Foote's Inverse Survivorship Analyses
durationFreq

Models of Sampling and Extinction for Taxonomic Duration Datasets
nearestNeighborDist

Nearest Neighbor Distances for Morphological Disparity Studies
probAnc

Probability of being a sampled ancestor of another sampled taxon
seqTimeList

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

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

Simulating Un-Conditioned Trees of Fossil Taxa
taxa2phylo

Convert Simulated Taxon Data into a Phylogeny
multiDiv

Calculating Diversity Curves Across Multiple Datasets
timeLadderTree

Resolve Polytomies by Order of First Appearance
dateNodes

Absolute Dates for Nodes of a Time-Scaled Phylogeny
paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution
simFossilTaxa

Simulating Taxa in the Fossil Record
SamplingConv

Converting Sampling Estimates
sampleRanges

Sampling Taxon Ranges
perCapitaRates

perCapitaRates
binTimeData

Bin Simulated Temporal Ranges in Discrete Intervals
horizonSampRate

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

Comparing the Time-Scaling of Trees
inverseSurv

Inverse Survivorship Models in the Fossil Record
reverseList

Reverse List Structure
timePaleoPhy

Timescaling of Paleo-Phylogenies
getSampProbDisc

Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges