Package: phylosignal 1.3.1

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://fkeck.r-universe.dev', 'https://cloud.r-project.org'))

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:

7.20 score 16 stars 100 scripts 309 downloads 39 mentions 40 exports 90 dependencies

Last updated 1 years agofrom:dfa59275a5. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 05 2024
R-4.5-win-x86_64	OK	Nov 05 2024
R-4.5-linux-x86_64	OK	Nov 05 2024
R-4.4-win-x86_64	OK	Nov 05 2024
R-4.4-mac-x86_64	OK	Nov 05 2024
R-4.4-mac-aarch64	OK	Nov 05 2024
R-4.3-win-x86_64	OK	Nov 05 2024
R-4.3-mac-x86_64	OK	Nov 05 2024
R-4.3-mac-aarch64	OK	Nov 05 2024

Exports:barplot.phylo4d descentsNames directDescents distEq dotplot dotplot.phylo4d evenColors focusStop focusTips focusTraits focusTree graphClust gridplot gridplot.phylo4d kStarTest kTest lambdaTest lipaMoran mantelStat matchTipsAndTraits moranTest multiplot.phylo4d pagelLogLik phyloCorrelogram phyloSignal phyloSignalBS phyloSignalINT phyloSim phyloSimSignal phyloWeights plot.graphclust plot.phylocorrelogram plot.phylosim plot.phylosimsignal print.graphclust print.phylosimsignal read.p4d rTraitContWeight subsetPhyloSimSignal white2red

Dependencies:ade4 adegenet adephylo ape askpass base64enc boot bslib cachem cli cluster colorspace commonmark cpp11 crayon curl DBI digest dplyr fansi farver fastmap fontawesome fs generics ggplot2 glue gtable hms htmltools httpuv httr igraph isoband jquerylib jsonlite labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl permute phylobase pillar pixmap pkgconfig plyr prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 rlang rncl RNeXML sass scales segmented seqinr shiny sourcetools sp stringi stringr sys tibble tidyr tidyselect utf8 uuid vctrs vegan viridisLite withr XML xml2 xtable

Package overview

Francois Keck

Rendered fromBasics.Rmdusingknitr::rmarkdownon Nov 05 2024.

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

Plotting functions

Francois Keck

Rendered fromDemo_plots.Rmdusingknitr::rmarkdownon Nov 05 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Set layout for plots	.layouterize
Set layout for plots	.layouterizeRatio
Reordering vector or matrix of settings.	.orderGrArg
Barplot of Traits Values along a Phylogeny	barplot.phylo4d
Names of descents	descentsNames
ID of direct descents	directDescents
Pairwise Distance from Regularly Distributed Points	distEq
Dotplot	dotplot
Dotplot of Traits Values along a Phylogeny	dotplot.phylo4d
Palette of evenly distributed colors	evenColors
Focus on sub parts of a plot	focusStop focusTips focusTraits focusTree
Phylogenetically constrained clustering	graphClust
Gridplot	gridplot
Gridplot of Traits Values along a Phylogeny	gridplot.phylo4d
Computes permutation test for Blomberg's K Star	kStarTest
Computes permutation test for Blomberg's K	kTest
Test Pagel's Lambda Optimize Pagel's Lambda and do a likelihood ratio test.	lambdaTest
Local Indicator of Phylogenetic Association	lipaMoran
Mantel statistic	mantelStat
Match matrix row/col names with phylo4d tips/traits	matchTipsAndTraits
Computes permutation test for Moran's I	moranTest
Plots of Traits Values along a Phylogeny	multiplot.phylo4d
Phylogeny and pollution sensitivity of diatoms	navic
Computes log-likelihood for data and a given value of Pagel's Lambda	pagelLogLik
Phylogenetic correlogram	phyloCorrelogram
phylosignal	phylosignal
Computes phylogenetic signal with different methods	phyloSignal
Computes phylogenetic signal for bootstrapped replicates of a phylogeny.	phyloSignalBS
Computes phylogenetic signal at each internal node of a phylogeny	phyloSignalINT
Simulate the behaviour of phylogenetic signal statistics with a given phylogeny	phyloSim
Phylogenetic signal estimation as a fraction of a Brownian Motion process.	phyloSimSignal
Phylogenetic weights matrix	phyloWeights
Plot phylogenetically constrained clustering	plot.graphclust
Plot a phylogenetic correlogram	plot.phylocorrelogram
Plot 'phylosim' object	plot.phylosim
Plot signal estimation as a fraction of a Brownian Motion process.	plot.phylosimsignal
#' Print results of phylogenetically constrained clustering	print.graphclust
Print signal estimation as a fraction of a Brownian Motion process.	print.phylosimsignal
Read a phylo4d object from files	read.p4d
Traits Values Simulation	rTraitContWeight
phyloSimSignal subsetting	subsetPhyloSimSignal
Color Palette	white2red