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

Functions

barplot.phylo4d Man page
descentsNames Man page
directDescents Man page
distEq Man page
dotplot Man page
dotplot.phylo4d Man page
evenColors Man page
focusStop Man page
focusTips Man page
focusTraits Man page
focusTree Man page
graphClust Man page
gridplot Man page
gridplot.phylo4d Man page
kStarTest Man page
kTest Man page
lambdaTest Man page
.layouterize Man page
.layouterizeRatio Man page
lipaMoran Man page
mantelStat Man page
matchTipsAndTraits Man page
moranTest Man page
multiplot.phylo4d Man page
navic Man page
.orderGrArg Man page
pagelLogLik Man page
phyloCorrelogram Man page
phylosignal Man page
phyloSignal Man page
phyloSignalBS Man page
phyloSignalINT Man page
phylosignal-package Man page
phyloSim Man page
phyloSimSignal Man page
phyloWeights Man page
plot.graphclust Man page
plot.phylocorrelogram Man page
plot.phylosim Man page
plot.phylosimsignal Man page
print.graphclust Man page
print.phylosimsignal Man page
read.p4d Man page
rTraitContWeight Man page
subsetPhyloSimSignal Man page
white2red Man page

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.