Paleontological and Phylogenetic Analyses of Evolution

Documentation for package ‘paleotree’ version 2.3

DESCRIPTION file.

Help Pages

A B C D E F G H I M N O P Q R S T U

paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution

-- A --

addTermBranchLength

Modify or Drop Terminal Branches of Various Types

-- B --

binTimeData	Bin Simulated Temporal Ranges in Discrete Intervals
bin_cal3TimePaleoPhy	Three Rate Calibrated Timescaling of Paleo-Phylogenies
bin_timePaleoPhy	Timescaling of Paleo-Phylogenies
branchClasses	Partitions the branch lengths of a tree into several classes based on their placement.

-- C --

cal3TimePaleoPhy	Three Rate Calibrated Timescaling of Paleo-Phylogenies
candleTaxa	Simulating Extinct Clades of Monophyletic Taxa
cladogeneticTraitCont	Simulate Cladogenetic Trait Evolution
collapseNodes	Randomly Collapse a Portion of Nodes on a Phylogeny
compareNodeAges	Comparing the Time-Scaling of Trees
compareTermBranches	Comparing the Time-Scaling of Trees
compareTimescaling	Comparing the Time-Scaling of Trees
constrainParPaleo	Constrain Parameters for a Model Function from paleotree

-- D --

dateNodes	Absolute Dates for Nodes of a Time-Scaled Phylogeny
deadTree	Simulating Extinct Clades of Monophyletic Taxa
degradeTree	Randomly Collapse a Portion of Nodes on a Phylogeny
depthRainbow	Paint Tree Branch Depth by Color
DiversityCurves	Diversity Curves
dropExtant	Modify or Drop Terminal Branches of Various Types
dropExtinct	Modify or Drop Terminal Branches of Various Types
dropPaleoTip	Modify or Drop Terminal Branches of Various Types
dropZLB	Modify or Drop Terminal Branches of Various Types
durationFreq	Models of Sampling and Extinction for Taxonomic Duration Datasets

-- E --

expandTaxonTree

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

-- F --

fixRootTime	Modify or Drop Terminal Branches of Various Types
footeValues	Calculates Values for Foote's Inverse Survivorship Analyses
freqRat	Frequency Ratio Method for Estimating Sampling Probability

-- G --

getSampProbDisc	Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges
getSampRateCont	Fit Models of Sampling Rates to Continuous-Time Taxon Ranges
graptCharMatrix	Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
graptDisparity	Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
graptDistMat	Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
graptRanges	Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea

-- H --

horizonSampRate

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

-- I --

inverseSurv	Inverse Survivorship Models in the Fossil Record
invSurv	Inverse Survivorship Models in the Fossil Record

-- M --

make_durationFreqCont	Models of Sampling and Extinction for Taxonomic Duration Datasets
make_durationFreqDisc	Models of Sampling and Extinction for Taxonomic Duration Datasets
make_inverseSurv	Inverse Survivorship Models in the Fossil Record
minBranchLength	Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
modelMethods	Model Function Methods: Parameter Names, Bounds and Initial Values
modifyTerminalBranches	Modify or Drop Terminal Branches of Various Types
multiDiv	Calculating Diversity Curves Across Multiple Datasets

-- N --

nearestNeighborDist

Nearest Neighbor Distances for Morphological Disparity Studies

-- O --

optimPaleo

Simplified Optimizer for paleotree Likelihood Functions

-- P --

paleotree	paleotree: Paleontological and Phylogenetic Analyses of Evolution
parbounds	Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds.constrained	Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds.paleotreeFunc	Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds<-	Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds<-.constrained	Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds<-.paleotreeFunc	Model Function Methods: Parameter Names, Bounds and Initial Values
parInit	Model Function Methods: Parameter Names, Bounds and Initial Values
parInit.constrained	Model Function Methods: Parameter Names, Bounds and Initial Values
parInit.paleotreeFunc	Model Function Methods: Parameter Names, Bounds and Initial Values
parLower	Model Function Methods: Parameter Names, Bounds and Initial Values
parLower.constrained	Model Function Methods: Parameter Names, Bounds and Initial Values
parLower.paleotreeFunc	Model Function Methods: Parameter Names, Bounds and Initial Values
parLower<-	Model Function Methods: Parameter Names, Bounds and Initial Values
parLower<-.constrained	Model Function Methods: Parameter Names, Bounds and Initial Values
parLower<-.paleotreeFunc	Model Function Methods: Parameter Names, Bounds and Initial Values
parnames	Model Function Methods: Parameter Names, Bounds and Initial Values
parnames.constrained	Model Function Methods: Parameter Names, Bounds and Initial Values
parnames.paleotreeFunc	Model Function Methods: Parameter Names, Bounds and Initial Values
parnames<-	Model Function Methods: Parameter Names, Bounds and Initial Values
parnames<-.constrained	Model Function Methods: Parameter Names, Bounds and Initial Values
parnames<-.paleotreeFunc	Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper	Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper.constrained	Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper.paleotreeFunc	Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper<-	Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper<-.constrained	Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper<-.paleotreeFunc	Model Function Methods: Parameter Names, Bounds and Initial Values
perCapitaRates	perCapitaRates
perfectParsCharTree	Simulate a Set of Parsimony-Informative Characters for a Phylogeny
phyloDiv	Diversity Curves
plotMultiDiv	Calculating Diversity Curves Across Multiple Datasets
plotTraitgram	Plot a Traitgram for Continuous Traits
pqr2Ps	Joint Probability of A Clade Surviving Infinitely or Being Sampled Once
pqsRate2sProb	Converting Sampling Estimates
probAnc	Probability of being a sampled ancestor of another sampled taxon

-- Q --

qsProb2Comp	Converting Sampling Estimates
qsRate2Comp	Converting Sampling Estimates

-- R --

retiolitinae	Cladogram and Range Data for the Retiolitinae
retioRanges	Cladogram and Range Data for the Retiolitinae
retioTree	Cladogram and Range Data for the Retiolitinae
reverseList	Reverse List Structure
rootSplit	Split Tip Taxa by Root Divergence

-- S --

sampleRanges	Sampling Taxon Ranges
SamplingConv	Converting Sampling Estimates
seqTimeList	Construct a Stochastic Sequenced Time-List from an Unsequenced Time-List
simCandleTaxa	Simulating Extinct Clades of Monophyletic Taxa
simFossilTaxa	Simulating Taxa in the Fossil Record
simFossilTaxa_SRCond	Simulating Taxa in the Fossil Record, Conditioned on Sampling Rate
simPaleoTrees	Simulating Un-Conditioned Trees of Fossil Taxa
simTermTaxa	Simulating Extinct Clades of Monophyletic Taxa
simTermTaxaAdvanced	Simulating Extinct Clades of Monophyletic Taxa
sProb2sRate	Converting Sampling Estimates
sRate2sProb	Converting Sampling Estimates

-- T --

taxa2cladogram	Convert Simulated Taxon Data into a Cladogram
taxa2phylo	Convert Simulated Taxon Data into a Phylogeny
taxicDivCont	Diversity Curves
taxicDivDisc	Diversity Curves
termTaxa	Simulating Extinct Clades of Monophyletic Taxa
timeLadderTree	Resolve Polytomies by Order of First Appearance
timePaleoPhy	Timescaling of Paleo-Phylogenies
timeSliceTree	Time-Slicing a Phylogeny
trueCandle	Simulating Extinct Clades of Monophyletic Taxa
trueTermTaxaTree	Simulating Extinct Clades of Monophyletic Taxa

-- U --

unitLengthTree

Scale Tree to Unit-Length