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]>

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picante/json (API)

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

Peer review:

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

Datasets:

On CRAN:

73 exports 32 stars 6.71 score 11 dependencies 14 dependents 414 mentions 900 scripts 3.9k downloads

Last updated 1 years agofrom:b891440afa. Checks:OK: 1 WARNING: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 12 2024
R-4.5-win-x86_64WARNINGAug 12 2024
R-4.5-linux-x86_64WARNINGAug 12 2024
R-4.4-win-x86_64WARNINGAug 12 2024
R-4.4-mac-x86_64WARNINGAug 12 2024
R-4.4-mac-aarch64WARNINGAug 12 2024
R-4.3-win-x86_64WARNINGAug 12 2024
R-4.3-mac-x86_64WARNINGAug 12 2024
R-4.3-mac-aarch64WARNINGAug 12 2024

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.ubcolor.plot.phylocomdistcomdistntcomm.phylo.corcomm.phylo.qrcor.tabledf2veceadevol.distinctexpected.pdinternal2tipsKcalcmatch.comm.distmatch.phylo.commmatch.phylo.datamatrix2samplemntdmpdmultiPhylosignalnode.agepblmpblmpredictpcdpdphyEstimatephyEstimateDiscphylosignalphylosorphylosor.rndphylostructpic.varianceprune.missingprune.samplepscpsdpsepsrpsvpsv.spprandomizeMatrixraoDreadsamplesample2matrixses.mntdses.mpdses.pdsortColumnssortRowsspecaccum.psrspecies.distsppregssppregs.plottax.distinctivenesstaxaShuffletipShuffletraitgramunifracvariance.pdwritesamplewritetraits

Dependencies:apeclusterdigestlatticeMASSMatrixmgcvnlmepermuteRcppvegan

Data and analysis in picante

Rendered frompicante-intro.Rnwusingutils::Sweaveon Aug 12 2024.

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

Readme and manuals

Help Manual

Help pageTopics
picante: Integrating Phylogenies and Ecologypicante-package picante
Color tip labels based on traitcolor.plot.phylo
Calculates inter-community mean pairwise distancecomdist
Calculates inter-community mean nearest taxon distancecomdistnn comdistnt
Correlations between species co-occurrence and phylogenetic distancescomm.phylo.cor
Quantile regression slopes between species co-occurrence and phylogenetic distancescomm.phylo.qr
Table of correlations and P-valuescor.table
Species' evolutionary distinctivenessevol.distinct
Expected PD, PD Variance, and Edge Abundance Distribution of a phylogenyead expected.pd variance.pd
Host-parasitoid food web dataIvesGodfray
K statistic of phylogenetic signalKcalc
Match taxa in phylogeny and datamatch.comm.dist match.phylo.comm match.phylo.data
Convert community data matrix to Phylocom samplematrix2sample
Mean nearest taxon distancemnnd mntd
Mean pairwise distancempd
Calculates phylogenetic signal for data.frame of traitsmultiPhylosignal
Phylogenetic Bipartite Linear Modelpblm pblmpredict
Phylogenetic Community DissimilarityPCD pcd
Calculate Faith's Phylogenetic Diversitypd
Phylogenetic estimation of traits for unobserved taxaphyEstimate phyEstimateDisc
Phylocom default dataphylocom
Measure phylogenetic signalphylosignal
Phylogenetic index of beta-diversity PhyloSorphylosor
Null PhyloSor values of phylogenetic beta-diversityphylosor.rnd
Permutations to Test for Phylogenetic Signal in Community Compositionphylostruct
Prune tree to match community data or trait dataprune.missing prune.sample
Phylogenetic Species Diversity Metricspsc psd pse psr psv psv.spp
Null models for community data matrix randomizationrandomizeMatrix
Rao's quadratic entropyraoD
Read Phylocom samplereadsample
Convert Phylocom sample to community data matrixsample2matrix
Standardized effect size of MNTDses.mnnd ses.mntd
Standardized effect size of MPDses.mpd
Standardized effect size of PDses.pd
Phylogenetic Species Richness Sample-Based Rarefaction Curvespecaccum.psr
Species co-occurrence distancesspecies.dist
Regressions to Separate Phylogenetic Attraction and Repulsionsppregs sppregs.plot
Taxonomic distinctiveness sensu Vane-Wright or Maytax.distinctiveness
Draw phylogeny with nodes at trait positionstraitgram
Unweighted UniFrac distance between communitiesunifrac
Picante utility functionsdf2vec internal2tips node.age pic.variance sortColumns sortRows taxaShuffle tipShuffle
Write a Phylocom community sample filewritesample
Write a Phylocom traits formatted filewritetraits