Package: phylosignal 1.3.1

Francois Keck

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.

Authors:Francois Keck <[email protected]>

phylosignal_1.3.1.tar.gz
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phylosignal.pdf |phylosignal.html✨
phylosignal/json (API)

# Install 'phylosignal' in R:
install.packages('phylosignal', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fkeck/phylosignal/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • navic - Phylogeny and pollution sensitivity of diatoms

On CRAN:

openblascpp

7.22 score 16 stars 103 scripts 366 downloads 39 mentions 40 exports 90 dependencies

Last updated 1 years agofrom:dfa59275a5. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 05 2024
R-4.5-win-x86_64OKDec 05 2024
R-4.5-linux-x86_64OKDec 05 2024
R-4.4-win-x86_64OKDec 05 2024
R-4.4-mac-x86_64OKDec 05 2024
R-4.4-mac-aarch64OKDec 05 2024
R-4.3-win-x86_64OKDec 05 2024
R-4.3-mac-x86_64OKDec 05 2024
R-4.3-mac-aarch64OKDec 05 2024

Exports:barplot.phylo4ddescentsNamesdirectDescentsdistEqdotplotdotplot.phylo4devenColorsfocusStopfocusTipsfocusTraitsfocusTreegraphClustgridplotgridplot.phylo4dkStarTestkTestlambdaTestlipaMoranmantelStatmatchTipsAndTraitsmoranTestmultiplot.phylo4dpagelLogLikphyloCorrelogramphyloSignalphyloSignalBSphyloSignalINTphyloSimphyloSimSignalphyloWeightsplot.graphclustplot.phylocorrelogramplot.phylosimplot.phylosimsignalprint.graphclustprint.phylosimsignalread.p4drTraitContWeightsubsetPhyloSimSignalwhite2red

Dependencies:ade4adegenetadephyloapeaskpassbase64encbootbslibcachemcliclustercolorspacecommonmarkcpp11crayoncurlDBIdigestdplyrfansifarverfastmapfontawesomefsgenericsggplot2gluegtablehmshtmltoolshttpuvhttrigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpermutephylobasepillarpixmappkgconfigplyrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrnclRNeXMLsassscalessegmentedseqinrshinysourcetoolsspstringistringrsystibbletidyrtidyselectutf8uuidvctrsveganviridisLitewithrXMLxml2xtable

Package overview

Francois Keck

Rendered fromBasics.Rmdusingknitr::rmarkdownon Dec 05 2024.

Last update: 2019-01-02
Started: 2018-01-09

Plotting functions

Francois Keck

Rendered fromDemo_plots.Rmdusingknitr::rmarkdownon Dec 05 2024.

Last update: 2019-01-02
Started: 2018-01-09

Readme and manuals

Help Manual

Help pageTopics
Set layout for plots.layouterize
Set layout for plots.layouterizeRatio
Reordering vector or matrix of settings..orderGrArg
Barplot of Traits Values along a Phylogenybarplot.phylo4d
Names of descentsdescentsNames
ID of direct descentsdirectDescents
Pairwise Distance from Regularly Distributed PointsdistEq
Dotplotdotplot
Dotplot of Traits Values along a Phylogenydotplot.phylo4d
Palette of evenly distributed colorsevenColors
Focus on sub parts of a plotfocusStop focusTips focusTraits focusTree
Phylogenetically constrained clusteringgraphClust
Gridplotgridplot
Gridplot of Traits Values along a Phylogenygridplot.phylo4d
Computes permutation test for Blomberg's K StarkStarTest
Computes permutation test for Blomberg's KkTest
Test Pagel's Lambda Optimize Pagel's Lambda and do a likelihood ratio test.lambdaTest
Local Indicator of Phylogenetic AssociationlipaMoran
Mantel statisticmantelStat
Match matrix row/col names with phylo4d tips/traitsmatchTipsAndTraits
Computes permutation test for Moran's ImoranTest
Plots of Traits Values along a Phylogenymultiplot.phylo4d
Phylogeny and pollution sensitivity of diatomsnavic
Computes log-likelihood for data and a given value of Pagel's LambdapagelLogLik
Phylogenetic correlogramphyloCorrelogram
phylosignalphylosignal
Computes phylogenetic signal with different methodsphyloSignal
Computes phylogenetic signal for bootstrapped replicates of a phylogeny.phyloSignalBS
Computes phylogenetic signal at each internal node of a phylogenyphyloSignalINT
Simulate the behaviour of phylogenetic signal statistics with a given phylogenyphyloSim
Phylogenetic signal estimation as a fraction of a Brownian Motion process.phyloSimSignal
Phylogenetic weights matrixphyloWeights
Plot phylogenetically constrained clusteringplot.graphclust
Plot a phylogenetic correlogramplot.phylocorrelogram
Plot 'phylosim' objectplot.phylosim
Plot signal estimation as a fraction of a Brownian Motion process.plot.phylosimsignal
#' Print results of phylogenetically constrained clusteringprint.graphclust
Print signal estimation as a fraction of a Brownian Motion process.print.phylosimsignal
Read a phylo4d object from filesread.p4d
Traits Values SimulationrTraitContWeight
phyloSimSignal subsettingsubsetPhyloSimSignal
Color Palettewhite2red