Exploring the Phylogenetic Signal in Continuous Traits
Barplot of Traits Values along a Phylogeny
Names of descents
ID of direct descents
Pairwise Distance from Regularly Distributed Points
Dotplot of Traits Values along a Phylogeny
Dotplot
Palette of evenly distributed colors
Focus on sub parts of a plot
Phylogenetically constrained clustering
Gridplot of Traits Values along a Phylogeny
Gridplot
Computes permutation test for Blomberg's K Star
Computes permutation test for Blomberg's K
Test Pagel's Lambda Optimize Pagel's Lambda and do a likelihood ratio ...
Set layout for plots
Set layout for plots
Local Indicator of Phylogenetic Association
Mantel statistic
Match matrix row/col names with phylo4d tips/traits
Computes permutation test for Moran's I
Plots of Traits Values along a Phylogeny
Reordering vector or matrix of settings.
Computes log-likelihood for data and a given value of Pagel's Lambda
Phylogenetic correlogram
phylosignal
Computes phylogenetic signal for bootstrapped replicates of a phylogen...
Computes phylogenetic signal at each internal node of a phylogeny
Computes phylogenetic signal with different methods
Simulate the behaviour of phylogenetic signal statistics with a given ...
Phylogenetic signal estimation as a fraction of a Brownian Motion proc...
Phylogenetic weights matrix
Plot phylogenetically constrained clustering
Plot a phylogenetic correlogram
Plot phylosim object
Plot signal estimation as a fraction of a Brownian Motion process.
#' Print results of phylogenetically constrained clustering
Print signal estimation as a fraction of a Brownian Motion process.
Read a phylo4d object from files
Traits Values Simulation
phyloSimSignal subsetting
Color Palette
A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.