phylosignal: Exploring the Phylogenetic Signal in Continuous Traits

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.

AuthorFrancois Keck <francois.keck@gmail.com>
Date of publication2015-10-26 15:58:53
MaintainerFrancois Keck <francois.keck@gmail.com>
LicenseGPL-3
Version1.1

View on CRAN

Man pages

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

focus: 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...

layouterize: Set layout for plots

layouterizeRatio: Set layout for plots

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

orderGrArg: Reordering vector or matrix of settings.

pagelLogLik: Computes log-likelihood for data and a given value of Pagel's...

phyloCorrelogram: Phylogenetic correlogram

phylosignal: phylosignal

phyloSignalBS: Computes phylogenetic signal for bootstrapped replicates of a...

phyloSignalINT: Computes phylogenetic signal at each internal node of a...

phylosignalStats: Computes phylogenetic signal with different methods

phyloSim: Simulate the behaviour of phylogenetic signal statistics with...

phyloSimSignal: Phylogenetic signal estimation as a fraction of a Brownian...

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...

print.graphclust: #' Print results of phylogenetically constrained clustering

print.phylosimsignal: Print signal estimation as a fraction of a Brownian Motion...

read.p4d: Read a phylo4d object from files

rTraitContWeight: Traits Values Simulation

subsetPhyloSimSignal: phyloSimSignal subsetting

white2red: Color Palette

Files in this package

phylosignal
phylosignal/src
phylosignal/src/Makevars
phylosignal/src/signaltest.cpp
phylosignal/src/Makevars.win
phylosignal/src/RcppExports.cpp
phylosignal/NAMESPACE
phylosignal/data
phylosignal/data/navic.RData
phylosignal/R
phylosignal/R/phyloSimSignal.R phylosignal/R/phyloSim.R phylosignal/R/phylosignal-package.R phylosignal/R/correlogram.R phylosignal/R/plotPhyloDisabled.R phylosignal/R/phyloSignal.R phylosignal/R/barPhylo.R phylosignal/R/graphClust.R phylosignal/R/phyloWeights.R phylosignal/R/utilities.R phylosignal/R/phyloSignalExtra.R phylosignal/R/RcppExports.R phylosignal/R/readp4d.R phylosignal/R/lipa.R
phylosignal/README.md
phylosignal/MD5
phylosignal/DESCRIPTION
phylosignal/man
phylosignal/man/lambdaTest.Rd phylosignal/man/white2red.Rd phylosignal/man/evenColors.Rd phylosignal/man/graphClust.Rd phylosignal/man/plot.graphclust.Rd phylosignal/man/distEq.Rd phylosignal/man/matchTipsAndTraits.Rd phylosignal/man/mantelStat.Rd phylosignal/man/subsetPhyloSimSignal.Rd phylosignal/man/descentsNames.Rd phylosignal/man/dotplot.Rd phylosignal/man/pagelLogLik.Rd phylosignal/man/layouterize.Rd phylosignal/man/focus.Rd phylosignal/man/plot.phylosim.Rd phylosignal/man/layouterizeRatio.Rd phylosignal/man/rTraitContWeight.Rd phylosignal/man/phyloWeights.Rd phylosignal/man/gridplot.Rd phylosignal/man/phylosignalStats.Rd phylosignal/man/plot.phylosimsignal.Rd phylosignal/man/moranTest.Rd phylosignal/man/plot.phylocorrelogram.Rd phylosignal/man/phyloSignalINT.Rd phylosignal/man/barplot.phylo4d.Rd phylosignal/man/read.p4d.Rd phylosignal/man/phylosignal.Rd phylosignal/man/gridplot.phylo4d.Rd phylosignal/man/print.graphclust.Rd phylosignal/man/orderGrArg.Rd phylosignal/man/print.phylosimsignal.Rd phylosignal/man/navic.Rd phylosignal/man/phyloCorrelogram.Rd phylosignal/man/phyloSignalBS.Rd phylosignal/man/multiplot.phylo4d.Rd phylosignal/man/dotplot.phylo4d.Rd phylosignal/man/directDescents.Rd phylosignal/man/kTest.Rd phylosignal/man/lipaMoran.Rd phylosignal/man/kStarTest.Rd phylosignal/man/phyloSim.Rd phylosignal/man/phyloSimSignal.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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