This is the very first tutorial for you in RevBayes. The goal of this set of tutorials is
getting you started and familiar with the basics in RevBayes. If you have some familiarity
with R or similar software, then this should be straight forward. Nevertheless, we recommend
you to work through these tutorials to learn all the specific quirks of RevBayes.
Continuous Variables
Over the full real line
Moves available in RevBayes for continuous variables.
Move
Description
Citation
mvMirror
mvRandomDive
mvSlice
mvSlide
mvSlideBactrian
Positive only (or negative only) continuous variables
Positive continuous variables, such as drawn from a Gamma, Exponental or Lognormal distribution, require moves that don’t change the sign.
In principle it is possible to apply also moves that work on the full real line, and then let the moves be rejected if they are outside the boundary, but this may be inefficient.
Moves available in RevBayes for positive continuous variables.
Move
Description
Citation
mvGammaScale
mvLevyJump
mvLevyJumpSum
mvMirrorMultiplier
mvScale
mvScaleBactrian
mvScaleBactrianCauchy
Multiple Continuous Variables
Moves available in RevBayes for positive continuous variables.
Move
Description
Citation
mvAVMVN
mvEllipticalSliceSamplingSimple
mvMultipleElementVectorScale
mvUpDownScale
mvShrinkExpand
mvShrinkExpandScale
mvUpDownScale
mvSynchronizedVectorFixedSingleElementSlide
mvUpDownSlide
mvUpDownSlideBactrian
mvVectorBinarySwitch
mvVectorFixedSingleElementSlide
mvVectorScale
mvVectorSingleElementSlide
mvVectorSlide
mvVectorSlideRecenter
GMRF and HSMRF
Moves available in RevBayes for positive continuous variables.
Move
Description
Citation
mvGMRFHyperpriorGibbs
mvGMRFUnevenGridHyperpriorGibbs
mvHSRFHyperpriorsGibbs
mvHSRFIntervalSwap
mvHSRFUnevenGridHyperpriorsGibbs
Matrices
Moves available in RevBayes for positive continuous variables.
Move
Description
Citation
mvConjugateInverseWishart
mvCorrelationMatrixElementSwap
mvCorrelationMatrixRandomWalk
mvCorrelationMatrixSingleElementBeta
mvCorrelationMatrixSpecificElementBeta
mvCorrelationMatrixUpdate
mvGraphFlipClique
mvGraphFlipEdge
mvGraphShiftEdge
mvMatrixElementScale
mvMatrixElementSlide
mvSymmetricMatrixElementSlide
Probabilities (numbers bounded between 0 and 1)
Moves available in RevBayes for integer and natural number variables.
Move
Description
Citation
mvBetaProbability
mvProbabilityElementScale
Simplices
Moves available in RevBayes for positive continuous variables.
Move
Description
Citation
mvBetaSimplex
mvDirichletSimplex
mvElementSwapSimplex
mvSimplex
mvSimplexElementScale
Natural and Integer numbers
Moves available in RevBayes for integer and natural number variables.
Move
Description
Citation
mvBinarySwitch
Flipping a value from 0 to 1 and vice versa
mvRandomGeometricWalk
mvRandomIntegerWalk
mvRandomNaturalWalk
Trees
Moves available in RevBayes for tree variables.
Move
Description
Citation
mvAddRemoveTip
mvBranchLengthScale
mvCollapseExpandFossilBranch
mvEmpiricalTree
mvFNPR
mvFossilTimeSlideUniform
mvGPR
mvIndependentTopology
mvNNI
mvNarrow
mvNodeTimeScale
mvNodeTimeSlideBeta
mvNodeTimeSlidePathTruncatedNormal
mvNodeTimeSlideUniform
mvNodeTimeSlideUniformAgeConstrained
mvResampleFBD
mvRootTimeScaleBactrian
mvRootTimeSlideUniform
mvSPR
mvSubtreeScale
mvSubtreeSwap
mvTipTimeSlideUniform
mvTreeScale
On trees and other variables
Moves available in RevBayes for tree variables.
Move
Description
Citation
mvGibbsDrawCharacterHistory
mvBirthDeathEvent
mvBirthDeathEventContinuous
mvBirthDeathEventDiscrete
mvBirthDeathFromAgeEvent
mvBurstEvent
mvCharacterHistory
mvContinuousEventScale
mvDiscreteEventCategoryRandomWalk
mvEventTimeBeta
mvEventTimeSlide
mvLayeredScaleProposal
mvNarrowExchangeRateMatrix
mvNodeRateTimeSlideBeta
mvNodeRateTimeSlideUniform
mvRateAgeBetaShift
mvRateAgeProposal
mvRateAgeSubtreeProposal
Species Trees
Moves available in RevBayes for tree variables.
Move
Description
Citation
mvSpeciesTreeScale
mvSpeciesNarrow
mvSpeciesNodeTimeSlideUniform
mvSpeciesSubtreeScale
mvSpeciesSubtreeScaleBeta
mvSpeciesTreeScale
Unassigned
Weird moves …
Moves available in RevBayes for positive continuous variables.