Package: RRphylo 3.0.2

Silvia Castiglione

RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

Functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.

Authors:Pasquale Raia [aut], Silvia Castiglione [aut, cre], Carmela Serio [aut], Giorgia Girardi [aut], Alessandro Mondanaro [aut], Marina Melchionna [aut], Mirko Di Febbraro [aut], Antonio Profico [aut], Francesco Carotenuto [aut]

RRphylo_3.0.2.tar.gz
RRphylo_3.0.2.zip(r-4.7)RRphylo_3.0.2.zip(r-4.6)RRphylo_3.0.2.zip(r-4.5)
RRphylo_3.0.2.tgz(r-4.6-any)RRphylo_3.0.2.tgz(r-4.5-any)
RRphylo_3.0.2.tar.gz(r-4.7-any)RRphylo_3.0.2.tar.gz(r-4.6-any)
RRphylo_3.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
RRphylo/json (API)

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

Bug tracker:https://github.com/pasraia/rrphylo/issues

Datasets:

On CRAN:

Conda:

8.69 score 11 stars 2 packages 104 scripts 754 downloads 9 mentions 52 exports 38 dependencies

Last updated from:b12cc19c7d. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK241
source / vignettesOK342
linux-release-x86_64OK190
macos-release-arm64OK270
macos-oldrel-arm64OK242
windows-develOK206
windows-releaseOK147
windows-oldrelOK164
wasm-releaseOK165

Exports:addShiftangle.matrixcolorbarcompRatesconv.mapcutPhylodistNodesevo.dirfix.polygetGenusgetMommygetSislollipoPlotmakeFossilmakeLmakeL1move.lineagenamesComparenode.pathsoverfitPGLSoverfitRRoverfitSCoverfitSSoverfitSTPGLS_fossilphyloclustplotConvplotRatesplotRRplotShiftplotTrendrandom.evolvability.testrate.maprateHistoryresampleTreerescaleRRretrieve.anglesRRphyloscaleTreesearch.convsearch.shiftsearch.trendsetBMsig2BMsizedsubtreeStableTraitsRswap.phyloswapONEtipstree.mergertreeComparetreedataMatch

Dependencies:apecliclusterGenerationcodacodetoolscombinatcpp11DEoptimdigestdoParallelemmeansestimabilityexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dvctrs

Phylogenetic tree manipulation
Index | tree.merger tool | tree.merger basics | Merging trees: input tree and data | Merging trees: Attaching individual tips to the backbone tree | Merging trees: Attaching clades to the backbone tree | Building a new tree | Guided examples | scaleTree tool | Guided examples | move.lineage tool | cutPhylo tool | fix.poly tool | References
Rendered fromTree-Manipulation.Rmdusingknitr::rmarkdown_notangle

Last update: 2025-07-11
Started: 2020-09-25

Creating alternative phylogenies from a starting tree
Index | swapONE | Swapping species positions | Shifting node ages | Guided examples | resampleTree | References
Rendered fromAlternative-trees.Rmdusingknitr::rmarkdown_notangle

Last update: 2025-03-22
Started: 2025-03-17

Testing RRphylo methods overfit
Index | overfit- functions basics | overfitRR | Guided examples | overfitSS | overfitST | overfitSC | overfitPGLS
Rendered fromoverfit.Rmdusingknitr::rmarkdown_notangle

Last update: 2025-03-22
Started: 2025-03-17

Plotting tools
Index | plotting RRphylo outputs onto the tree | plotting RRphylo rates | plotting search.trend results | plotting search.shift results | plotting search.conv results
Rendered fromPlotting-tools.Rmdusingknitr::rmarkdown_notangle

Last update: 2025-03-22
Started: 2024-08-09

RRphylo
Index | RRphylo Basics | RRphylo phylogenetic ridge regression | Accounting for the effect of a covariate | Multiple regression framework | Setting values at internal nodes | Guided examples | References
Rendered fromRRphylo.Rmdusingknitr::rmarkdown_notangle

Last update: 2025-03-22
Started: 2020-06-26

Searching for morphological convergence
Index | search.conv basics | Morphological convergence between clades | Morphological convergence within/between categories | Guided examples | References
Rendered fromsearch.conv.Rmdusingknitr::rmarkdown_notangle

Last update: 2025-03-22
Started: 2020-07-22

Searching for temporal trends in phenotypes or rates
Index | search.trend basics | Temporal trends on the entire tree | Temporal trends at clade level | Multivariate data and multiple RRphylo output | Guided examples | References
Rendered fromsearch.trend.Rmdusingknitr::rmarkdown_notangle

Last update: 2025-03-22
Started: 2020-07-22

Searching for rate shifts
Index | search.shift basics | Clade condition | Sparse condition | Guided examples | References
Rendered fromsearch.shift.Rmdusingknitr::rmarkdown_notangle

Last update: 2025-03-17
Started: 2020-07-22

Readme and manuals

Help Manual

Help pageTopics
Phylogenetic Ridge Regression Methods for Comparative StudiesRRphylo-package
Ontogenetic shape vectors analysisangle.matrix
Draw colorbar on a plotcolorbar
Comparing average absolute rates between cladescompRates
Mapping morphological convergence on 3D surfacesconv.map
Cut the phylogeny at a given age or nodecutPhylo
Example datasetDataApes
Example datasetDataCetaceans
Example datasetDataFelids
Example datasetDataOrnithodirans
Example datasetDataSimians
Example datasetDataUng
Finding distance between nodes and tipsdistNodes
Phylogenetic vector analysis of phenotypic changeevo.dir
Resolving polytomies to non-zero length branchesfix.poly
Taxonomic inspection of the tree at the genus levelgetGenus
Upward tip or node to root pathgetMommy
Get sister cladegetSis
Lollipop chartslollipoPlot
Make fossil species on a phylogenymakeFossil
Matrix of branch lengths along root-to-tip pathsmakeL
Matrix of branch lengths along a root-to-node pathmakeL1
Move tips or cladesmove.lineage
Checking species names for misspelling and synonymsnamesCompare
Tracing nodes along pathsnode.paths
Testing PGLS_fossil overfitoverfitPGLS
Testing RRphylo overfitoverfitRR
Testing search.conv overfitoverfitSC
Testing search.shift overfitoverfitSS
Testing search.trend overfitoverfitST
Phylogenetic Generalized Least Square with phylogenies including fossilsPGLS_fossil
Test for phylogenetic clusteringphyloclust
Graphical representation of search.conv resultsplotConv
Plot RRphylo rates at a specified nodeplotRates
Plot the RRphylo output onto the phylogenetic treeplotRR
Graphical representation of search.shift resultsaddShift plotShift
Graphical representation of search.trend resultsplotTrend
Randomization test for phylogenetic structuring in evolvabilityrandom.evolvability.test
Mapping rate and direction of phenotypic change on 3D surfaces.rate.map
Computing historical ratesrateHistory
Altering phylogenetic treesresampleTree
Rescaling phylogenetic treesrescaleRR
Extracting a user-specified subset of the evo.dir resultsretrieve.angles
Evolutionary rates computation along phylogeniesRRphylo
Defunct functions in Package RRphyloRRphylo-defunct swap.phylo
Deprecated functions in Package RRphyloRRphylo-deprecated
Phylogenetic tree calibrationscaleTree
Searching for morphological convergence among species and cladessearch.conv
Locating shifts in phenotypic evolutionary ratessearch.shift
Searching for evolutionary trends in phenotypes and ratessearch.trend
Producing simulated phenotypes with trendssetBM
Brownian Motion rate computationsig2BM
Find a node subtending to a clade of desired sizesizedsubtree
Run StableTraits from within RStableTraitsR
Create alternative phylogenies from a given treeswapONE
Get descending tipstips
Fast construction of phylogenetic treestree.merger
Visualize the difference between phylogenetic treestreeCompare
Cross-reference tree and datatreedataMatch