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 phytools: Phylogenetic Tools for Comparative Biology (and Other Things)
 paintSubTree: Paint subtrees with a discrete character
Paint subtrees with a discrete character
Description
This function maps or "paints" an arbitrary, i.e., userspecified, discrete character history on the tree. paintSubTree
paints the clade downstream of node
with a particular state; whereas paintBranches
paints only a specified branch.
Usage
1 2  paintSubTree(tree, node, state, anc.state="1", stem=FALSE)
paintBranches(tree, edge, state, anc.state="1")

Arguments
tree 
a phylogenetic tree as an object of class 
node 
an integer specifying the node number tipward of which the function should paint the derived state. 
edge 
an integer or vector of integers specifying the node or tip numbers of the edges that should be painted in 
state 
a string (or numeric value) specifying the state to paint on the tree tipward of 
anc.state 
the ancestral state to use; will only be applied if there are presently no character values mapped on the tree. 
stem 
logical or numeric value indicating whether to use the derived state on the stem leading to 
Value
A modified phylogenetic tree of class "phylo"
with the following additional elements:
maps 
a list of named vectors containing the times spent in each state on each branch, in the order in which they occur. 
mapped.edge 
a matrix containing the total time spent in each state along each edge of the tree. 
Author(s)
Liam Revell liam.revell@umb.edu
References
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217223.
See Also
make.simmap
, read.simmap
, plotSimmap
, sim.history
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 add.arrow: Add an arrow pointing to a tip or node on the tree
 add.color.bar: Add color bar to a plot
 add.everywhere: Add tip to all edges in a tree
 add.random: Add tips at random to the tree
 add.simmap.legend: Add legend to stochastically mapped tree
 add.species.to.genus: Add species to genus on a phylogeny or bind simulated species...
 aic.w: Computes AIC weights
 allFurcTrees: Generate all bi and multifurcating unrooted trees
 anc.Bayes: Bayesian ancestral character estimation
 anc.ML: Ancestral character estimation using likelihood
 ancThresh: Ancestral character estimation under the threshold model...
 anc.trend: Ancestral character estimation with a trend
 anoletree: Phylogeny of Greater Antillean anole ecomorph species with...
 applyBranchLengths: Applies the branch lengths of a reference tree to a target
 as.multiPhylo: Conversion to object of class '"multiPhylo"'
 averageTree: Compute an average tree from a set of trees and related...
 ave.rates: Average the posterior rates
 bd: Convert object of class "birthdeath" to raw birth & death...
 bind.tip: Attaches a new tip to a tree
 bind.tree.simmap: Attaches a new tip to a tree
 bmPlot: Simulates and visualizes discretetime Brownian evolution on...
 branching.diffusion: Animation of branching random diffusion
 brownie.lite: Likelihood test for rate variation in a continuous trait
 brownieREML: REML version of brownie.lite
 cladelabels: Add labels to subtrees of a plotted phylogeny
 collapse.to.star: Collapse a subtree to a star phylogeny
 collapseTree: Interactive tree visualizer
 consensus.edges: Compute consensus edges for a tree under some criterion
 contMap: Map continuous trait evolution on the tree
 cophylo: Creates a cophylogenetic plot
 cospeciation: Conducts a statistical test of cospeciation between two trees
 countSimmap: Counts the number of character changes on a SIMMAP style tree...
 densityMap: Plot posterior density of stochastic mapping on a tree
 densityTree: Plots a posterior sample of trees
 describe.simmap: Summarizes a stochastic mapped tree or set of trees
 di2multi.simmap: Collapse branches of zero length to polytomy in stochastic...
 dotTree: Creates a phylogenetic dot plot
 drop.clade: Drop a clade from a tree
 drop.leaves: Drop all the leaves (tips) from a tree
 drop.tip.contMap: Drop tip or tips from an object of class "contMap" or...
 drop.tip.simmap: Drop tips or extract clade from tree with mapped discrete...
 edgeProbs: Compute the relative frequencies of state changes along edges
 estDiversity: Estimate diversity at each node of the tree
 evol.rate.mcmc: Bayesian MCMC method for identifying exceptional phenotypic...
 evol.vcv: Likelihood test for variation in the evolutionary VCV matrix
 evolvcv.lite: Likelihood test for a shift in the evolutionary correlation...
 exhaustiveMP: Exhaustive and branch & bound MP optimization
 expm: Matrix exponential
 export.as.xml: Export trees & data in XML format
 fancyTree: Plots special types of phylogenetic trees
 fastAnc: Fast estimation of ML ancestral states
 fastBM: Fast Brownian simulation
 fastMRCA: Get the MRCA (or height above the root of the MRCA) of a pair...
 findMRCA: Get the MRCA of a set of taxa
 fitBayes: Evolutionary model fitting with intraspecific variability...
 fitDiversityModel: Fit diversitydependent phenotypic evolution model
 fitMk: Fits Mk model
 fitPagel: Function to test for correlated evolution of binary traits
 gammatest: Gamma test of Pybus & Harvey (2000)
 genSeq: Simulate a DNA alignment on the tree under a model
 getCladesofSize: Get all subtrees larger than or equal to a specified size
 getDescendants: Get descendant node numbers
 getExtant: Returns a list of the extant or extinct lineages in a tree...
 getSisters: Get the sister node number, label, or set of nodes for a node...
 getStates: Get the states at nodes or tips from a mapped tree
 ladderize.simmap: Ladderize a tree with a mapped discrete character
 lambda.transform: Lambda transformation of matrix
 likMlambda: Likelihood for joint lambda
 locate.fossil: Locate a fossil lineage in a tree using continuous characters
 locate.yeti: Locate a cryptic, recently extinct, or missing taxon on a...
 ls.tree: Least squares branch lengths for a given tree
 ltt: Creates lineagethroughtime plot (including extinct...
 ltt95: Creates a (1alpha)percent CI for a set of LTTs
 make.era.map: Create "era" map on a phylogenetic tree
 make.simmap: Simulate stochastic character maps on a phylogenetic tree or...
 map.overlap: Proportional overlap between two mapped character histories...
 mapped.states: Returns a vector, matrix, or list of the mapped states on a...
 map.to.singleton: Converts a mapped tree to a tree with singleton nodes
 markChanges: Add marked changes to a plotted tree with mapped discrete...
 matchNodes: Matches nodes between two trees
 mergeMappedStates: Merge two or more mapped states into one state
 midpoint.root: Midpoint root a phylogeny
 minRotate: Rotates all nodes of the tree to minimize the difference in...
 minSplit: Finding the minimum (median) split in the posterior sample
 modified.Grafen: Computes modified Grafen edge lengths
 mrp.supertree: Matrix representation parsimony supertree estimation
 multiC: Returns a list with phylogenetic VCV matrix for each mapped...
 multi.mantel: Multiple matrix regression (partial Mantel test)
 multiRF: Computes RobinsonFoulds distance between a set of trees
 nodeHeights: Compute the heights above the root of each node
 nodelabels.cophylo: Add labels to a plotted "cophylo" object
 optim.phylo.ls: Phylogeny inference using the least squares method
 orderMappedEdge: Order the columns of mapped.edge to match across trees
 paintSubTree: Paint subtrees with a discrete character
 paste.tree: Paste two trees together
 pbtree: Simulate purebirth or birthdeath stochastic tree or trees
 pgls.Ives: Phylogenetic regression with intraspecific sampling error
 phenogram: Plot phenogram (traitgram)
 phylANOVA: Phylogenetic ANOVA and posthoc tests
 phyl.cca: Phylogenetic canonical correlation analysis
 phyloDesign: Compute design matrix for least squares analyses
 phylo.heatmap: Creates a phylogenetic heat map
 phylomorphospace: Creates phylomorphospace plot
 phylomorphospace3d: Creates treedimensional phylomorphospace plot
 phylosig: Compute phylogenetic signal with two methods
 phylo.toBackbone: Converts tree to backbone or vice versa
 phylo.to.map: Plot tree with tips linked to geographic coordinates
 phyl.pairedttest: Phylogenetic paired ttest
 phyl.pca: Phylogenetic principal components analysis
 phyl.resid: Phylogenetic sizecorrection via GLS regression
 phyl.RMA: Phylogenetic reduced major axis (RMA) regression
 phyl.vcv: Compute evolutionary VCV matrix for a tree & dataset
 phytoolspackage: phytools: Phylogenetic Tools for comparative biology (and...
 plot.backbonePhylo: Plots backbone tree with triangles as clades
 plotBranchbyTrait: Plot branch colors by a quantitative trait or value
 plotSimmap: Plot stochastic character mapped tree
 plotThresh: Tree plotting with posterior probabilities of ancestral...
 plotTree: Plots rooted phylogenetic tree
 plotTree.wBars: Plot a tree with bars at the tips
 posterior.evolrate: Analysis of the posterior sample from evol.rate.mcmc
 print.backbonePhylo: Print method for backbone phylogeny
 ratebystate: Method for investigating the rate of one trait as a function...
 rateshift: Find the temporal position of one or more rate shifts
 read.newick: Robust Newick style tree reader
 read.simmap: Read SIMMAP style trees from file
 reorder.backbonePhylo: Reorders a backbone phylogeny
 reorderSimmap: Reorder edges of a simmap tree
 rep.phylo: Replicate a tree or set of trees
 reroot: Reroot a tree along an edge
 rerootingMethod: Get marginal ancestral state reconstructions by rerooting
 rescaleSimmap: Rescale SIMMAP style tree
 resolveNode: Compute all possible resolutions of a node or all nodes in a...
 rotateNodes: Rotates a node or set of nodes in a phylogenetic tree
 roundBranches: Rounds the branch lengths of a tree
 roundPhylogram: Plot a round phylogram
 rstate: Pick a random state according to a vector of probabilities
 sampleFrom: Sample from a set of distributions
 setMap: Set color map for objects of class '"contMap"' or...
 sim.corrs: Multivariate Brownian simulation with multiple correlations...
 sim.history: Simulate stochastic character history under some model
 sim.ratebystate: Conduct simulation of state dependent rate variation
 sim.rates: Brownian simulation with multiple evolutionary rates
 skewers: Matrix comparison using the method of random skewers
 splitEdgeColor: Split edge colors when descendant edges have different mapped...
 splitplotTree: Plots a phylogeny in two columns
 splitTree: Split tree at a point
 starTree: Create star phylogeny
 strahlerNumber: Computes Strahler number for trees and nodes
 threshBayes: Threshold model using Bayesian MCMC
 threshDIC: Deviance Information Criterion from the threshold model
 threshState: Computes value for a threshold character from a liability and...
 to.matrix: Convert a character vector to a binary matrix
 treeSlice: Slices the tree at a particular point and returns all...
 untangle: Attempts to untangle crossing branches for plotting
 vcvPhylo: Calculates cophenetic (i.e., phylogenetic VCV) matrix
 writeAncestors: Write a tree to file with ancestral states and (optionally)...
 writeNexus: Write a tree to file in Nexus format
 write.simmap: Write a stochastic character mapped tree to file