Package: RRphylo 2.8.1

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, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto

RRphylo_2.8.1.tar.gz
RRphylo_2.8.1.zip(r-4.5)RRphylo_2.8.1.zip(r-4.4)RRphylo_2.8.1.zip(r-4.3)
RRphylo_2.8.1.tgz(r-4.4-any)RRphylo_2.8.1.tgz(r-4.3-any)
RRphylo_2.8.1.tar.gz(r-4.5-noble)RRphylo_2.8.1.tar.gz(r-4.4-noble)
RRphylo_2.8.1.tgz(r-4.4-emscripten)RRphylo_2.8.1.tgz(r-4.3-emscripten)
RRphylo.pdf |RRphylo.html✨
RRphylo/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

7.46 score 10 stars 81 scripts 442 downloads 9 mentions 45 exports 37 dependencies

Last updated 3 months agofrom:589eff9bdb. Checks:OK: 5 NOTE: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 09 2024
R-4.5-winOKOct 09 2024
R-4.5-linuxOKOct 09 2024
R-4.4-winOKOct 09 2024
R-4.4-macOKOct 09 2024
R-4.3-winNOTEOct 09 2024
R-4.3-macNOTEOct 09 2024

Exports:addShiftangle.matrixcolorbarconv.mapcutPhylodistNodesevo.dirfix.polygetGenusgetMommygetSislollipoPlotmakeFossilmakeLmakeL1move.lineagenamesComparenode.pathsoverfitRRPGLS_fossilphyloclustplotConvplotRatesplotRRplotShiftplotTrendrandom.evolvability.testrate.maprescaleRRretrieve.anglesRRphyloscaleTreesearch.convsearch.shiftsearch.trendsetBMsig2BMsizedsubtreeStableTraitsRswap.phyloswapONEtipstree.mergertreeComparetreedataMatch

Dependencies:apecliclusterGenerationcodacodetoolscombinatcpp11DEoptimdigestdoParallelemmeansestimabilityexpmforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dvctrs

Testing RRphylo methods overfit

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromoverfitRR.Rmdusingknitr::rmarkdown_notangleon Oct 09 2024.

Last update: 2024-08-09
Started: 2020-06-26

Plotting tools

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromPlotting-tools.Rmdusingknitr::rmarkdown_notangleon Oct 09 2024.

Last update: 2024-08-09
Started: 2024-08-09

RRphylo

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromRRphylo.Rmdusingknitr::rmarkdown_notangleon Oct 09 2024.

Last update: 2024-08-10
Started: 2020-06-26

Searching for morphological convergence

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromsearch.conv.Rmdusingknitr::rmarkdown_notangleon Oct 09 2024.

Last update: 2024-08-10
Started: 2020-07-22

Searching for rate shifts

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromsearch.shift.Rmdusingknitr::rmarkdown_notangleon Oct 09 2024.

Last update: 2024-08-10
Started: 2020-07-22

Searching for temporal trends in phenotypes or rates

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromsearch.trend.Rmdusingknitr::rmarkdown_notangleon Oct 09 2024.

Last update: 2024-08-10
Started: 2020-07-22

Creating alternative phylogenetic hypotheses from a starting tree

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromswapONE.Rmdusingknitr::rmarkdown_notangleon Oct 09 2024.

Last update: 2024-08-09
Started: 2020-07-22

Phylogenetic tree manipulation

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromTree-Manipulation.Rmdusingknitr::rmarkdown_notangleon Oct 09 2024.

Last update: 2024-08-10
Started: 2020-09-25

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
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 RRphylo methods overfitoverfitRR
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
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 addition of tips and clades on an existing treetree.merger
Visualize the difference between phylogenetic treestreeCompare
Cross-reference tree and datatreedataMatch