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'))

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

Datasets:

DataApes - Example dataset
DataCetaceans - Example dataset
DataFelids - Example dataset
DataOrnithodirans - Example dataset
DataSimians - Example dataset
DataUng - Example dataset

On CRAN:

45 exports 10 stars 2.72 score 56 dependencies 9 mentions 80 scripts 562 downloads

Last updated 1 months agofrom:589eff9bdb. Checks:OK: 5 NOTE: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Sep 09 2024
R-4.5-win	OK	Sep 09 2024
R-4.5-linux	OK	Sep 09 2024
R-4.4-win	OK	Sep 09 2024
R-4.4-mac	OK	Sep 09 2024
R-4.3-win	NOTE	Sep 09 2024
R-4.3-mac	NOTE	Sep 09 2024

Exports:addShift angle.matrix colorbar conv.map cutPhylo distNodes evo.dir fix.poly getGenus getMommy getSis lollipoPlot makeFossil makeL makeL1 move.lineage namesCompare node.paths overfitRR PGLS_fossil phyloclust plotConv plotRates plotRR plotShift plotTrend random.evolvability.test rate.map rescaleRR retrieve.angles RRphylo scaleTree search.conv search.shift search.trend setBM sig2BM sizedsubtree StableTraitsR swap.phylo swapONE tips tree.merger treeCompare treedataMatch

Dependencies:ape cli clusterGeneration coda codetools colorspace combinat cpp11 DEoptim digest doParallel emmeans estimability expm fansi farver fastmatch foreach generics ggplot2 ggseqlogo glue gtable igraph isoband iterators labeling lattice lifecycle magrittr maps MASS Matrix mgcv mnormt munsell mvtnorm nlme numDeriv optimParallel phangorn phytools pillar pkgconfig quadprog R6 RColorBrewer Rcpp rlang scales scatterplot3d tibble utf8 vctrs viridisLite withr

Testing RRphylo methods overfit

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromoverfitRR.Rmdusingknitr::rmarkdown_notangleon Sep 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 Sep 09 2024.

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

RRphylo

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered fromRRphylo.Rmdusingknitr::rmarkdown_notangleon Sep 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 Sep 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 Sep 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 Sep 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 Sep 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 Sep 09 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Phylogenetic Ridge Regression Methods for Comparative Studies	RRphylo-package
Ontogenetic shape vectors analysis	angle.matrix
Draw colorbar on a plot	colorbar
Mapping morphological convergence on 3D surfaces	conv.map
Cut the phylogeny at a given age or node	cutPhylo
Example dataset	DataApes
Example dataset	DataCetaceans
Example dataset	DataFelids
Example dataset	DataOrnithodirans
Example dataset	DataSimians
Example dataset	DataUng
Finding distance between nodes and tips	distNodes
Phylogenetic vector analysis of phenotypic change	evo.dir
Resolving polytomies to non-zero length branches	fix.poly
Taxonomic inspection of the tree at the genus level	getGenus
Upward tip or node to root path	getMommy
Get sister clade	getSis
Lollipop charts	lollipoPlot
Make fossil species on a phylogeny	makeFossil
Matrix of branch lengths along root-to-tip paths	makeL
Matrix of branch lengths along a root-to-node path	makeL1
Move tips or clades	move.lineage
Checking species names for misspelling and synonyms	namesCompare
Tracing nodes along paths	node.paths
Testing RRphylo methods overfit	overfitRR
Phylogenetic Generalized Least Square with phylogenies including fossils	PGLS_fossil
Test for phylogenetic clustering	phyloclust
Graphical representation of search.conv results	plotConv
Plot RRphylo rates at a specified node	plotRates
Plot the RRphylo output onto the phylogenetic tree	plotRR
Graphical representation of search.shift results	addShift plotShift
Graphical representation of search.trend results	plotTrend
Randomization test for phylogenetic structuring in evolvability	random.evolvability.test
Mapping rate and direction of phenotypic change on 3D surfaces.	rate.map
Rescaling phylogenetic trees	rescaleRR
Extracting a user-specified subset of the evo.dir results	retrieve.angles
Evolutionary rates computation along phylogenies	RRphylo
Defunct functions in Package RRphylo	RRphylo-defunct swap.phylo
Deprecated functions in Package RRphylo	RRphylo-deprecated
Phylogenetic tree calibration	scaleTree
Searching for morphological convergence among species and clades	search.conv
Locating shifts in phenotypic evolutionary rates	search.shift
Searching for evolutionary trends in phenotypes and rates	search.trend
Producing simulated phenotypes with trends	setBM
Brownian Motion rate computation	sig2BM
Find a node subtending to a clade of desired size	sizedsubtree
Run StableTraits from within R	StableTraitsR
Create alternative phylogenies from a given tree	swapONE
Get descending tips	tips
Fast addition of tips and clades on an existing tree	tree.merger
Visualize the difference between phylogenetic trees	treeCompare
Cross-reference tree and data	treedataMatch

Usage by other packages (reverse dependencies)