Paleontological and Phylogenetic Analyses of Evolution

Documentation for package ‘paleotree’ version 3.0.0

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

paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution

-- A --

addTermBranchLength	Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
ammoniteTraitsRaia	Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
ammoniteTreeRaia	Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
ancPropStateMat	Estimating the Minimum Number of Character Transitions Using Maximum Parsimony

-- B --

bindPaleoTip	Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
binTimeData	Bin Simulated Temporal Ranges in Discrete Intervals
bin_cal3TimePaleoPhy	Three Rate Calibrated 'a posteriori' Time-Scaling of Paleo-Phylogenies
bin_timePaleoPhy	Typical 'a posteriori' Time-Scaling Approaches For Paleontological Phylogenies
branchClasses	Partitions the branch lengths of a tree into several classes based on their placement.

-- C --

cal3	Three Rate Calibrated 'a posteriori' Time-Scaling of Paleo-Phylogenies
cal3TimePaleoPhy	Three Rate Calibrated 'a posteriori' Time-Scaling of Paleo-Phylogenies
candleTaxa	Simulating Extinct Clades of Monophyletic Taxa
ceratopsianTreeRaia	Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
cervidTreeRaia	Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
charMatDicrano	Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
cladogeneticTraitCont	Simulate Cladogenetic Trait Evolution
cladogramDicrano	Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
cleanNewPhylo	Test the Edge Matrix of a 'phylo' Phylogeny Object for Inconsistencies
cleanTree	Test the Edge Matrix of a 'phylo' Phylogeny Object for Inconsistencies
collapseNodes	Randomly Collapse a Portion of Nodes on a Phylogeny
communityEcology	Miscellaneous Functions for Community Ecology
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
createMrBayesConstraints	Transform a Topology into a Set of Constraint Commands for MrBayes
createMrBayesTipCalibrations	Construct A Block of Tip Age Calibrations for Use with Tip-Dating Analyses in MrBayes
createMrBayesTipDatingNexus	Construct a Fully Formatted NEXUS Script for Performing Tip-Dating Analyses With MrBayes

-- 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
divCurveFossilRecordSim	Diversity-Curve Plotting for Simulations of Diversification and Sampling In the Fossil Record
DiversityCurves	Diversity Curves
dropExtant	Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
dropExtinct	Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
dropPaleoTip	Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
dropZLB	Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
durationFreq	Models of Sampling and Extinction for Taxonomic Duration Datasets

-- E --

equation2function	Turn a Character String of the Right-Hand Side of an Equation into an R Function
expandTaxonTree	Extrapolating Lower-Level Taxon Phylogenies from Higher-Level Taxon Trees

-- F --

fixRootTime	Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
footeValues	Calculates Values for Foote's Inverse Survivorship Analyses
foramAL	Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
foramALb	Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
foramAM	Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
foramAMb	Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
fossilRecord2fossilRanges	Methods for Editing or Converting Output from simFossilRecord
fossilRecord2fossilTaxa	Methods for Editing or Converting Output from simFossilRecord
fourDate2timeList	Converting Datasets of Taxon Ranges in Intervals Between timeList format and fourDate format
fourDateFunctions	Converting Datasets of Taxon Ranges in Intervals Between timeList format and fourDate format
freqRat	Frequency Ratio Method for Estimating Sampling Probability

-- G --

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
graptOccPBDB	Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
graptPBDB	Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
graptRanges	Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
graptTaxaPBDB	Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database

-- H --

horizonSampRate	Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 1997)
HurlbertPIE	Miscellaneous Functions for Community Ecology

-- I --

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

-- K --

kanto

Example Species Abundances Tables

-- M --

macroperforateForam	Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
makePBDBtaxonTree	Creating a Taxon-Tree from Taxonomic Data Downloaded from the Paleobiology Database
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
minCharChange	Estimating the Minimum Number of Character Transitions Using Maximum Parsimony
modelMethods	Model Function Methods: Parameter Names, Bounds and Initial Values
modifyTerminalBranches	Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
multiDiv	Calculating Diversity Curves Across Multiple Datasets

-- N --

nearestNeighborDist

Nearest Neighbor Distances for Morphological Disparity Studies

-- O --

obtainDatedPosteriorTreesMrB	Get the Sample of Posterior Trees from a Dated Phylogenetic Analysis with MrBayes (Or a Summary Tree, such as the MCCT)
occData2timeList	Converting Occurrences Data to a timeList Data Object
optimPaleo	Simplified Optimizer for paleotree Likelihood Functions

-- P --

pairwiseSpearmanRho	Miscellaneous Functions for Community Ecology
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
parentChild2taxonTree	Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table of Parent-Child Taxon Relationships
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
plotOccData	Plotting Occurrence Data Across Taxa
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 --

RaiaCopesRule	Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
resolveTreeChar	Resolve Polytomies Using Parsimony-Based Reconstruction of a Discrete Character
retioChar	Cladogram and Range Data for the Retiolitinae
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
setRootAge	Place a Non-Ultrametric Tree of Fossil Taxa on Absolute Time
setRootAges	Place a Non-Ultrametric Tree of Fossil Taxa on Absolute Time
shellSize	Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
simCandleTaxa	Simulating Extinct Clades of Monophyletic Taxa
simFossilRecord	Full-Scale Simulations of the Fossil Record with Birth, Death and Sampling of Morphotaxa
simFossilRecordMethods	Methods for Editing or Converting Output from simFossilRecord
simTermTaxa	Simulating Extinct Clades of Monophyletic Taxa
simTermTaxaAdvanced	Simulating Extinct Clades of Monophyletic Taxa
SongZhangDicrano	Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
sProb2sRate	Converting Sampling Estimates
sRate2sProb	Converting Sampling Estimates
sutureComplexity	Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015

-- T --

taxa2cladogram	Convert Simulated Taxon Data into a Cladogram
taxa2phylo	Convert Simulated Taxon Data into a Phylogeny
taxicDivCont	Diversity Curves
taxicDivDisc	Diversity Curves
taxonSortPBDBocc	Sorting Unique Taxa of a Given Rank from Paleobiology Database Occurrence Data
taxonTable2taxonTree	Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Hierarchical Table of Taxonomy Memberships
termTaxa	Simulating Extinct Clades of Monophyletic Taxa
testEdgeMat	Test the Edge Matrix of a 'phylo' Phylogeny Object for Inconsistencies
timeLadderTree	Resolve Polytomies by Order of First Appearance
timeList2fourDate	Converting Datasets of Taxon Ranges in Intervals Between timeList format and fourDate format
timePaleoPhy	Typical 'a posteriori' Time-Scaling Approaches For Paleontological Phylogenies
timeSliceFossilRecord	Methods for Editing or Converting Output from simFossilRecord
timeSliceTree	Time-Slicing a Phylogeny
tipdating	Construct a Fully Formatted NEXUS Script for Performing Tip-Dating Analyses With MrBayes
treeContradiction	Measure the Contradiction Difference Between Two Phylogenetic Topologies
trueCandle	Simulating Extinct Clades of Monophyletic Taxa
trueTermTaxaTree	Simulating Extinct Clades of Monophyletic Taxa

-- U --

unitLengthTree

Scale Tree to Unit-Length