phylosignal: Exploring the Phylogenetic Signal in Continuous Traits

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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.

Author
Francois Keck <francois.keck@gmail.com>
Date of publication
2015-10-26 15:58:53
Maintainer
Francois Keck <francois.keck@gmail.com>
License
GPL-3
Version
1.1

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