API for paleotree
Paleontological and Phylogenetic Analyses of Evolution

Global functions
DiversityCurves Man page
HurlbertPIE Man page Man page Source code
RaiaCopesRule Man page
SamplingConv Man page
Sankoff_character Source code
SongZhangDicrano Man page
accioBestAcquisitionModel Man page Source code
accioExhaustionCurve Man page Source code
accio_branch_order_with_stratigraphy Source code
accio_data_from_nexus_file Source code
accio_matrix_tree_from_ape_tree Source code
accio_matrix_tree_from_vector_tree Source code
accio_max_zipf_decay Source code
accio_min_and_max_lognormal_mag_given_hS Source code
accio_minimum_alpha_for_gamma_one Source code
accio_minimum_steps_history Source code
accio_patristic_distance_from_base Source code
addTermBranchLength Man page Man page Source code
ammoniteTraitsRaia Man page
ammoniteTreeRaia Man page
anagEvent Source code
ancPropStateMat Man page Man page Source code
bifurcEvent Source code
binTimeData Man page Source code
bin_cal3TimePaleoPhy Man page Man page Source code
bin_timePaleoPhy Man page Man page Source code
bindPaleoTip Man page Source code
branchClasses Man page Source code
buddingEvent Source code
buildContrastPoly Source code
cal3 Man page
cal3TimePaleoPhy Man page Source code
candleTaxa Man page
ceratopsianTreeRaia Man page
cervidTreeRaia Man page
charEdge2numeric Source code
charExhaustPlot Man page Source code
charMatDicrano Man page
checkFossilRecord Source code
cladogeneticTraitCont Man page Source code
cladogramDicranoX12 Man page
cladogramDicranoX13 Man page
cleanNewPhylo Man page Man page Source code
cleanTree Man page
collapseNodes Man page Source code
communityEcology Man page
compareNodeAges Man page Source code
compareTermBranches Man page Man page Source code
compareTimescaling Man page
constrainParPaleo Man page Source code
constrainParsePaleo Source code
contiguousIntegerSeq Source code
convert_letter_state_to_numeric Source code
createMrBayesConstraints Man page Source code
createMrBayesTipCalibrations Man page Source code
createMrBayesTipDatingNexus Man page Source code
create_quantile_vector Source code
crypticEvent Source code
dateNodes Man page Source code
date_taxa_on_tree_simple Source code
deadTree Man page Man page Source code
degradeTree Man page Source code
depthRainbow Man page Source code
distribution_loglikelihood_mul Source code
divCurveFossilRecordSim Man page Source code
draw_symmetric_axes Source code
dropExtant Man page Man page Source code
dropExtinct Man page Man page Source code
dropPaleoTip Man page Source code
dropZLB Man page Source code
durationFreq Man page
equation2function Man page Source code
eventOccurs Source code
exhaustionFunctions Man page
expandConstrainForm Source code
expandTaxonTree Man page Source code
expected_abundances Source code
expected_exhaustion_curve Source code
expected_sampled_richness Source code
expected_sampling_curve Source code
extEvent Source code
fisher_plot Source code
fixRootTime Man page Man page Source code
footeValues Man page Source code
foramAL Man page
foramALb Man page
foramAM Man page
foramAMb Man page
fossilRecord2fossilRanges Man page Man page Source code
fossilRecord2fossilTaxa Man page Man page Source code
fossilTaxa2fossilRecord Man page Source code
fourDate2timeList Man page Source code
fourDateFunctions Man page
freqRat Man page Source code
gamma_distribution Source code
geometric_distribution Source code
getMrBFixedAgesFromNexus Source code
getPosteriorProbabiities Source code
getRateMatrix Source code
getRootID Source code
getRunVitals Source code
getTaxaNames Source code
getTaxonDurations Source code
getUltimateAnc Source code
graptCharMatrix Man page
graptDisparity Man page
graptDistMat Man page
graptOccPBDB Man page
graptPBDB Man page
graptRanges Man page
graptTaxaPBDB Man page
horizonSampRate Man page Source code
initiateTaxa Source code
insertRow Source code
invSurv Man page
inverseSurv Man page
isTimeListSequential Source code
jack5_Fisher Source code
kanto Man page
loglikelihood_gamma_one_rad Source code
loglikelihood_geometric_rad Source code
loglikelihood_lognormal_rad Source code
loglikelihood_lognormal_rad_for_optim Source code
loglikelihood_zipf_rad Source code
lognormal_distribution Source code
macroperforateForam Man page
makeEmptyMorphNexusMrB Source code
makeIngroupConstraintMrB Source code
makeMrBayesBlock Source code
makePBDBtaxonTree Man page Source code
makeParFunct Source code
make_durationFreqCont Man page Source code
make_durationFreqDisc Man page Man page Source code
make_inverseSurv Man page Source code
make_paleotreeFunc Source code
minBranchLength Man page Source code
minCharChange Man page Source code
modelMethods Man page
modified_AIC Source code
modifyTerminalBranches Man page
multiDiv Man page Source code
nContradiction Source code
nearestNeighborDist Man page Source code
newTaxon Source code
nodeDates2branchLengths Man page Source code
obtainDatedPosteriorTreesMrB Man page Source code
occData2timeList Man page Source code
optimPaleo Man page Source code
optimize_gamma_one_abundance Source code
optimize_gamma_one_abundance_given_hS Source code
optimize_geometric_abundance Source code
optimize_lognormal_abundance Source code
optimize_lognormal_abundance_given_hS Source code
optimize_uniform_abundance Source code
optimize_zipf_abundance Source code
optimize_zipf_abundance_given_hS Source code
origination Source code
pairwiseSpearmanRho Man page Source code
paleotree Man page
paleotree-package Man page
parInit Man page Man page Source code
parInit.constrained Man page Man page Source code
parInit.paleotreeFunc Man page Man page Source code
parLower Man page Man page Source code
parLower.constrained Man page Man page Source code
parLower.paleotreeFunc Man page Man page Source code
parLower<- Man page
parLower<-.constrained Man page
parLower<-.paleotreeFunc Man page
parUpper Man page Man page Source code
parUpper.constrained Man page Man page Source code
parUpper.paleotreeFunc Man page Man page Source code
parUpper<- Man page
parUpper<-.constrained Man page
parUpper<-.paleotreeFunc Man page
parbounds Man page Man page Source code
parbounds.constrained Man page Man page Source code
parbounds.paleotreeFunc Man page Man page Source code
parbounds<- Man page
parbounds<-.constrained Man page
parbounds<-.paleotreeFunc Man page
parentChild2taxonTree Man page Source code
parnames Man page Source code
parnames.constrained Man page Man page Source code
parnames.paleotreeFunc Man page Man page Source code
parnames<- Man page
parnames<-.constrained Man page
parnames<-.paleotreeFunc Man page
parseNexusFile Source code
perCapitaRates Man page Source code
perfectParsCharTree Man page Source code
phyloDiv Man page Man page Source code
plotMultiDiv Man page Man page Source code
plotOccData Man page Source code
plotTraitgram Man page Source code
pqr2Ps Man page Source code
pqsRate2sProb Man page Man page Source code
probAnc Man page Source code
pullOccListData Source code
qsProb2Comp Man page Man page Source code
qsRate2Comp Man page Man page Source code
queryMissingParents Source code
ravel_polymorph Source code
read_nexus_tree Source code
resolveTreeChar Man page Source code
resolveTreeCharMechanism Source code
retioChar Man page
retioRanges Man page
retioTree Man page
retiolitinae Man page
reverseList Man page Source code
rootSplit Man page Source code
sProb2sRate Man page Source code
sRate2sProb Man page Man page Source code
sampEvent Source code
sampleRanges Man page Source code
sampleSeqVitals Source code
seqTimeList Man page Source code
setRootAge Man page Source code
setRootAges Man page Source code
shellSize Man page
simCandleTaxa Man page
simFossilRecord Man page Source code
simFossilRecordMethods Man page
simTermTaxa Man page Source code
simTermTaxaAdvanced Man page Man page Source code
sutureComplexity Man page
taxa2cladogram Man page Source code
taxa2phylo Man page Source code
taxicDivCont Man page Source code
taxicDivDisc Man page Man page Source code
taxonSortPBDBocc Man page Source code
taxonTable2taxonTree Man page Source code
termTaxa Man page
termination Source code
testContinue Source code
testContradiction Source code
testEdgeMat Man page Source code
testFinal Source code
testParentChild Source code
testTimeList Source code
testVitalsRecord Source code
timeLadderTree Man page Source code
timeList2fourDate Man page Source code
timePaleoPhy Man page Source code
timeSliceFossilRecord Man page Source code
timeSliceTree Man page Source code
tipdating Man page
translatePBDBocc Source code
translatePBDBtaxa Source code
treeContradiction Man page Source code
trueCandle Man page
trueTermTaxaTree Man page Man page Source code
twoWayEcologyCluster Man page Source code
unitLengthTree Man page Source code
unravel_polymorph Source code
whichLive Source code
whichSampled Source code
whichSampledInPast Source code
worthCheckingVitalsRecord Source code
writeSimpleSumtNexus Source code
zipf_distribution Source code
paleotree documentation built on Oct. 2, 2018, 5:04 p.m.