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 |
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 |
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 |
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 |
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 |
trueCandle |
Simulating Extinct Clades of Monophyletic Taxa |
trueTermTaxaTree |
Simulating Extinct Clades of Monophyletic Taxa |