Paleontological and Phylogenetic Analyses of Evolution

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Documentation for package ‘paleotree’ version 3.4.5

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paleotree-package paleotree: Paleontological and Phylogenetic Analyses of Evolution

-- A --

accioBestAcquisitionModel Analyses of the exhaustion of Character States Over Evolutionary History
accioExhaustionCurve Analyses of the exhaustion of Character States Over Evolutionary History
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_ Dating of Paleontological Phylogenies
bin_timePaleoPhy Simplistic _a posteriori_ Dating 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_ Dating of Paleontological Phylogenies
cal3TimePaleoPhy Three Rate Calibrated _a posteriori_ Dating of Paleontological 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
charExhaustPlot Analyses of the exhaustion of Character States Over Evolutionary History
charMatDicrano Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
cladogeneticTraitCont Simulate Cladogenetic Trait Evolution
cladogramDicranoX12 Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
cladogramDicranoX13 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
dateTaxonTreePBDB Date a Taxon-Topology from the Paleobiology Database Using Appearance Data from the API
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
exhaustionFunctions Analyses of the exhaustion of Character States Over Evolutionary History
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 Simulated Fossil Record Objects
fossilRecord2fossilTaxa Methods for Editing or Converting Output from Simulated Fossil Record Objects
fossilTaxa2fossilRecord Methods for Editing or Converting Output from Simulated Fossil Record Objects
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 --

getCladeTaxaPBDB Obtaining Data for Taxa or Occurrences From Paleobiology Database API
getDataPBDB Obtaining Data for Taxa or Occurrences From Paleobiology Database API
getPBDBocc Obtaining Data for Taxa or Occurrences From Paleobiology Database API
getSpecificTaxaPBDB Obtaining Data for Taxa or Occurrences From Paleobiology Database API
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
graptTimeTree Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
graptTree 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
minBranchLen Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
minBranchLength Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
minCharChange Estimating the Minimum Number of Character Transitions Using Maximum Parsimony
minimumBranchLen Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
minimumBranchLength Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
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
nodeDates2branchLengths Obtaining Edge Lengths for Undated Phylogenies Using Known Branching Node and Tip Ages

-- 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 Instantaneous _per-Capita_ Rates of Origination and Extinction from the Fossil Record
perfectParsCharTree Simulate a Set of Parsimony-Informative Characters for a Phylogeny
phyloDiv Diversity Curves
PIE Miscellaneous Functions for Community Ecology
plotMultiDiv Calculating Diversity Curves Across Multiple Datasets
plotOccData Plotting Occurrence Data Across Taxa
plotPhyloPicTree Plot a Phylogeny with Organismal Silhouettes from PhyloPic, Called Via the Paleobiology Database API
plotTaxaTreePBDB Creating a Taxon-Tree from Taxonomic Data Downloaded from the Paleobiology Database
plotTraitgram Plot a Traitgram for Continuous Traits
pqr2Ps Joint Probability of A Clade Surviving Infinitely or Being Sampled Once
pqsRate2sProb Converting Sampling Estimates
ProbabilityInterspecificEncounter Miscellaneous Functions for Community Ecology
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 Simulated Fossil Record Objects
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 Simplistic _a posteriori_ Dating Approaches For Paleontological Phylogenies
timeSliceFossilRecord Methods for Editing or Converting Output from Simulated Fossil Record Objects
timeSliceTree Time-Slicing a Phylogeny
tipdating Construct a Fully Formatted NEXUS Script for Performing Tip-Dating Analyses With MrBayes
tipDatingCompatabilitySummaryMrB Get the Compatibility Summary Topology From a Tip-Dating Analysis 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
twoWayEcologyCluster R-Mode vs Q-Mode Two-Way Cluster Analyses and Abundance Plot for Community Ecology Data

-- U --

unitLengthTree Scale Tree to Unit-Length