This package is considered a duplicate. The official version of this package is found at:https://skembel.r-universe.dev/picante

Package: picante 1.8.3

Steven W. Kembel

picante: Integrating Phylogenies and Ecology

Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.

Authors:Steven W. Kembel <[email protected]>, David D. Ackerly <[email protected]>, Simon P. Blomberg <[email protected]>, Will K. Cornwell <[email protected]>, Peter D. Cowan <[email protected]>, Matthew R. Helmus <[email protected]>, Helene Morlon <[email protected]>, Campbell O. Webb <[email protected]>

picante_1.8.3.tar.gz
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picante_1.8.3.tgz(r-4.6-x86_64)picante_1.8.3.tgz(r-4.6-arm64)picante_1.8.3.tgz(r-4.5-x86_64)picante_1.8.3.tgz(r-4.5-arm64)
picante_1.8.3.tar.gz(r-4.7-arm64)picante_1.8.3.tar.gz(r-4.7-x86_64)picante_1.8.3.tar.gz(r-4.6-arm64)picante_1.8.3.tar.gz(r-4.6-x86_64)
picante_1.8.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
picante/json (API)

# Install 'picante' in R:

install.packages('picante', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/skembel/picante/issues

Datasets:

IvesGodfray - Host-parasitoid food web data
phylocom - Phylocom default data

On CRAN:

11.83 score 39 stars 13 packages 1.6k scripts 8.2k downloads 414 mentions 73 exports 11 dependencies

Last updated from:b891440afa. Checks:11 WARNING, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	WARNING	154
linux-devel-x86_64	WARNING	136
source / vignettes	OK	196
linux-release-arm64	WARNING	158
linux-release-x86_64	WARNING	153
macos-release-arm64	WARNING	98
macos-release-x86_64	WARNING	229
macos-oldrel-arm64	WARNING	101
macos-oldrel-x86_64	WARNING	234
windows-devel	WARNING	101
windows-release	WARNING	102
windows-oldrel	WARNING	101
wasm-release	OK	151

Exports:.binomial.pd .edge.children.var .edge.children.var.ub .evolve.trait .extract.clade.noreord .get.nodes .match.tree .node.desc .node.number .phylosor.richness .phylosor.taxaShuffle .var.pd .var.pd.ub color.plot.phylo comdist comdistnt comm.phylo.cor comm.phylo.qr cor.table df2vec ead evol.distinct expected.pd internal2tips Kcalc match.comm.dist match.phylo.comm match.phylo.data matrix2sample mntd mpd multiPhylosignal node.age pblm pblmpredict pcd pd phyEstimate phyEstimateDisc phylosignal phylosor phylosor.rnd phylostruct pic.variance prune.missing prune.sample psc psd pse psr psv psv.spp randomizeMatrix raoD readsample sample2matrix ses.mntd ses.mpd ses.pd sortColumns sortRows specaccum.psr species.dist sppregs sppregs.plot tax.distinctiveness taxaShuffle tipShuffle traitgram unifrac variance.pd writesample writetraits

Dependencies:ape cluster digest lattice MASS Matrix mgcv nlme permute Rcpp vegan

Data and analysis in picante

Rendered frompicante-intro.Rnwusingutils::Sweave

Last update: 2019-03-18
Started: 2013-10-29

Help page	Topics
picante: Integrating Phylogenies and Ecology	picante-package picante
Color tip labels based on trait	color.plot.phylo
Calculates inter-community mean pairwise distance	comdist
Calculates inter-community mean nearest taxon distance	comdistnn comdistnt
Correlations between species co-occurrence and phylogenetic distances	comm.phylo.cor
Quantile regression slopes between species co-occurrence and phylogenetic distances	comm.phylo.qr
Table of correlations and P-values	cor.table
Species' evolutionary distinctiveness	evol.distinct
Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny	ead expected.pd variance.pd
Host-parasitoid food web data	IvesGodfray
K statistic of phylogenetic signal	Kcalc
Match taxa in phylogeny and data	match.comm.dist match.phylo.comm match.phylo.data
Convert community data matrix to Phylocom sample	matrix2sample
Mean nearest taxon distance	mnnd mntd
Mean pairwise distance	mpd
Calculates phylogenetic signal for data.frame of traits	multiPhylosignal
Phylogenetic Bipartite Linear Model	pblm pblmpredict
Phylogenetic Community Dissimilarity	PCD pcd
Calculate Faith's Phylogenetic Diversity	pd
Phylogenetic estimation of traits for unobserved taxa	phyEstimate phyEstimateDisc
Phylocom default data	phylocom
Measure phylogenetic signal	phylosignal
Phylogenetic index of beta-diversity PhyloSor	phylosor
Null PhyloSor values of phylogenetic beta-diversity	phylosor.rnd
Permutations to Test for Phylogenetic Signal in Community Composition	phylostruct
Prune tree to match community data or trait data	prune.missing prune.sample
Phylogenetic Species Diversity Metrics	psc psd pse psr psv psv.spp
Null models for community data matrix randomization	randomizeMatrix
Rao's quadratic entropy	raoD
Read Phylocom sample	readsample
Convert Phylocom sample to community data matrix	sample2matrix
Standardized effect size of MNTD	ses.mnnd ses.mntd
Standardized effect size of MPD	ses.mpd
Standardized effect size of PD	ses.pd
Phylogenetic Species Richness Sample-Based Rarefaction Curve	specaccum.psr
Species co-occurrence distances	species.dist
Regressions to Separate Phylogenetic Attraction and Repulsion	sppregs sppregs.plot
Taxonomic distinctiveness sensu Vane-Wright or May	tax.distinctiveness
Draw phylogeny with nodes at trait positions	traitgram
Unweighted UniFrac distance between communities	unifrac
Picante utility functions	df2vec internal2tips node.age pic.variance sortColumns sortRows taxaShuffle tipShuffle
Write a Phylocom community sample file	writesample
Write a Phylocom traits formatted file	writetraits

Package: picante 1.8.3

picante: Integrating Phylogenies and Ecology

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)