.layouterize            Set layout for plots
.layouterizeRatio       Set layout for plots
.orderGrArg             Reordering vector or matrix of settings.
barplot.phylo4d         Barplot of Traits Values along a Phylogeny
descentsNames           Names of descents
directDescents          ID of direct descents
distEq                  Pairwise Distance from Regularly Distributed
                        Points
dotplot                 Dotplot
dotplot.phylo4d         Dotplot of Traits Values along a Phylogeny
evenColors              Palette of evenly distributed colors
focusTraits             Focus on sub parts of a plot
graphClust              Phylogenetically constrained clustering
gridplot                Gridplot
gridplot.phylo4d        Gridplot of Traits Values along a Phylogeny
kStarTest               Computes permutation test for Blomberg's K Star
kTest                   Computes permutation test for Blomberg's K
lambdaTest              Test Pagel's Lambda Optimize Pagel's Lambda and
                        do a likelihood ratio test.
lipaMoran               Local Indicator of Phylogenetic Association
mantelStat              Mantel statistic
matchTipsAndTraits      Match matrix row/col names with phylo4d
                        tips/traits
moranTest               Computes permutation test for Moran's I
multiplot.phylo4d       Plots of Traits Values along a Phylogeny
navic                   Phylogeny and pollution sensitivity of diatoms
pagelLogLik             Computes log-likelihood for data and a given
                        value of Pagel's Lambda
phyloCorrelogram        Phylogenetic correlogram
phyloSignal             Computes phylogenetic signal with different
                        methods
phyloSignalBS           Computes phylogenetic signal for bootstrapped
                        replicates of a phylogeny.
phyloSignalINT          Computes phylogenetic signal at each internal
                        node of a phylogeny
phyloSim                Simulate the behaviour of phylogenetic signal
                        statistics with a given phylogeny
phyloSimSignal          Phylogenetic signal estimation as a fraction of
                        a Brownian Motion process.
phyloWeights            Phylogenetic weights matrix
phylosignal             phylosignal
plot.graphclust         Plot phylogenetically constrained clustering
plot.phylocorrelogram   Plot a phylogenetic correlogram
plot.phylosim           Plot 'phylosim' object
plot.phylosimsignal     Plot signal estimation as a fraction of a
                        Brownian Motion process.
print.graphclust        #' Print results of phylogenetically
                        constrained clustering
print.phylosimsignal    Print signal estimation as a fraction of a
                        Brownian Motion process.
rTraitContWeight        Traits Values Simulation
read.p4d                Read a phylo4d object from files
subsetPhyloSimSignal    phyloSimSignal subsetting
white2red               Color Palette
