phylosignal: Exploring the Phylogenetic Signal in Continuous Traits
Version 1.1

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("phylosignal")

Getting started

README.md

Popular man pages

dotplot: Dotplot
evenColors: Palette of evenly distributed colors
lambdaTest: Test Pagel's Lambda Optimize Pagel's Lambda and do a...
multiplot.phylo4d: Plots of Traits Values along a Phylogeny
phylosignalStats: Computes phylogenetic signal with different methods
phyloSim: Simulate the behaviour of phylogenetic signal statistics with...
plot.phylocorrelogram: Plot a phylogenetic correlogram
See all...

All man pages Function index File listing

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

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

Files

src
src/Makevars
src/signaltest.cpp
src/Makevars.win
src/RcppExports.cpp
NAMESPACE
data
data/navic.RData
R
R/phyloSimSignal.R
R/phyloSim.R
R/phylosignal-package.R
R/correlogram.R
R/plotPhyloDisabled.R
R/phyloSignal.R
R/barPhylo.R
R/graphClust.R
R/phyloWeights.R
R/utilities.R
R/phyloSignalExtra.R
R/RcppExports.R
R/readp4d.R
R/lipa.R
README.md
MD5
DESCRIPTION
man
man/lambdaTest.Rd
man/white2red.Rd
man/evenColors.Rd
man/graphClust.Rd
man/plot.graphclust.Rd
man/distEq.Rd
man/matchTipsAndTraits.Rd
man/mantelStat.Rd
man/subsetPhyloSimSignal.Rd
man/descentsNames.Rd
man/dotplot.Rd
man/pagelLogLik.Rd
man/layouterize.Rd
man/focus.Rd
man/plot.phylosim.Rd
man/layouterizeRatio.Rd
man/rTraitContWeight.Rd
man/phyloWeights.Rd
man/gridplot.Rd
man/phylosignalStats.Rd
man/plot.phylosimsignal.Rd
man/moranTest.Rd
man/plot.phylocorrelogram.Rd
man/phyloSignalINT.Rd
man/barplot.phylo4d.Rd
man/read.p4d.Rd
man/phylosignal.Rd
man/gridplot.phylo4d.Rd
man/print.graphclust.Rd
man/orderGrArg.Rd
man/print.phylosimsignal.Rd
man/navic.Rd
man/phyloCorrelogram.Rd
man/phyloSignalBS.Rd
man/multiplot.phylo4d.Rd
man/dotplot.phylo4d.Rd
man/directDescents.Rd
man/kTest.Rd
man/lipaMoran.Rd
man/kStarTest.Rd
man/phyloSim.Rd
man/phyloSimSignal.Rd
phylosignal documentation built on May 19, 2017, 11:11 p.m.

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