# Exploring the Phylogenetic Signal in Continuous Traits

## Documentation for package ‘phylosignal’ version 1.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

phylosignal-package | phylosignal
.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
focusStop | Focus on sub parts of a plot
focusTips | Focus on sub parts of a plot
focusTraits | Focus on sub parts of a plot
focusTree | 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
phylosignal | phylosignal
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
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.
read.p4d | Read a phylo4d object from files
rTraitContWeight | Traits Values Simulation
subsetPhyloSimSignal | phyloSimSignal subsetting
white2red | Color Palette