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 |
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 |
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. |
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 |
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 |
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 |
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 |
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 |
horizonSampRate | Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 1997) |
HurlbertPIE | Miscellaneous Functions for Community Ecology |
inverseSurv | Inverse Survivorship Models in the Fossil Record |
invSurv | Inverse Survivorship Models in the Fossil Record |
kanto | Example Species Abundances Tables |
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 |
nearestNeighborDist | Nearest Neighbor Distances for Morphological Disparity Studies |
nodeDates2branchLengths | Obtaining Edge Lengths for Undated Phylogenies Using Known Branching Node and Tip Ages |
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 |
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 |
qsProb2Comp | Converting Sampling Estimates |
qsRate2Comp | Converting Sampling Estimates |
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 |
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 |
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 |
unitLengthTree | Scale Tree to Unit-Length |