Package: phylolm 2.6.7

Lam Si Tung Ho

phylolm: Phylogenetic Linear Regression

Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.

Authors:Lam Si Tung Ho [aut, cre], Cecile Ane [aut], Robert Lachlan [ctb], Kelsey Tarpinian [ctb], Rachel Feldman [ctb], Qing Yu [ctb], Wouter van der Bijl [ctb], Joan Maspons [ctb], Rutger Vos [ctb], Paul Bastide [ctb], Ana Marcia Barbosa [ctb]

phylolm_2.6.7.tar.gz
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phylolm.pdf |phylolm.html✨
phylolm/json (API)

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

Peer review:

Bug tracker:https://github.com/lamho86/phylolm/issues

Datasets:
  • flowerSize - Flower size of 25 Euphorbiaceae species
  • flowerTree - Phylogenetic tree of 25 Euphorbiaceae species
  • guidetree - Binary population tree within Arabidopsis thaliana
  • quartetCF - Quartet concordance factors across Arabidopsis thaliana

On CRAN:

10.74 score 32 stars 14 packages 330 scripts 6.1k downloads 47 mentions 44 exports 11 dependencies

Last updated 2 months agofrom:87b812a379. Checks:OK: 3 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 03 2024
R-4.5-win-x86_64OKDec 03 2024
R-4.5-linux-x86_64OKDec 03 2024
R-4.4-win-x86_64NOTEDec 03 2024
R-4.4-mac-x86_64NOTEDec 03 2024
R-4.4-mac-aarch64NOTEDec 03 2024
R-4.3-win-x86_64NOTEDec 03 2024
R-4.3-mac-x86_64NOTEDec 03 2024
R-4.3-mac-aarch64NOTEDec 03 2024

Exports:AIC.logLik.phyloglmAIC.logLik.phylolmAIC.phyloglmAIC.phylolmconfint.phylolmextractAIC.phylolmlogLik.phyloglmlogLik.phylolmmacemodel.frame.phylolmnobs.phyloglmnobs.phylolmOU1d.loglikOUshiftsphyloglmphyloglmstepphylolmphylostepplot.OUshiftsplot.phyloglmplot.phylolmpredict.phyloglmpredict.phylolmprint.logLik.phyloglmprint.logLik.phylolmprint.phyloglmprint.phylolmprint.summary.phyloglmprint.summary.phylolmpruningwise.branching.timespruningwise.distFromRootrbinTraitresiduals.phyloglmresiduals.phylolmrTraitstepwise.test.treesummary.phyloglmsummary.phylolmtest.one.species.treetest.tree.preparationthree.point.computetransf.branch.lengthsvcov.phyloglmvcov.phylolm

Dependencies:apecodetoolsdigestfuturefuture.applyglobalslatticelistenvnlmeparallellyRcpp

Readme and manuals

Help Manual

Help pageTopics
Phylogenetic Linear Regressionphylolm-package
Flower size of 25 Euphorbiaceae speciesflowerSize
Phylogenetic tree of 25 Euphorbiaceae speciesflowerTree
Binary population tree within Arabidopsis thalianaguidetree
Multi-task learning for ancestral state estimation.mace
Log likelihood of an one-dimensional Ornstein-Uhlenbeck modelOU1d.loglik
Detections of shifts in the OU process along a phylogeny.OUshifts
Methods for class 'OUshifts'.plot.OUshifts
Phylogenetic Generalized Linear Modelphyloglm
Methods for class 'phyloglm'.AIC.logLik.phyloglm AIC.phyloglm logLik.phyloglm nobs.phyloglm plot.phyloglm predict.phyloglm print.logLik.phyloglm print.phyloglm print.summary.phyloglm residuals.phyloglm summary.phyloglm vcov.phyloglm
Stepwise model selection for Phylogenetic Generalized Linear Modelphyloglmstep
Phylogenetic Linear Modelphylolm
Methods for class 'phylolm'.AIC.logLik.phylolm AIC.phylolm confint.phylolm extractAIC.phylolm logLik.phylolm model.frame.phylolm nobs.phylolm plot.phylolm predict.phylolm print.logLik.phylolm print.phylolm print.summary.phylolm residuals.phylolm summary.phylolm vcov.phylolm
Stepwise model selection for Phylogenetic Linear Modelphylostep
Calculates internal node ages in an ultrametric "pruningwise" treepruningwise.branching.times
Calculates node distance from the root in an "pruningwise" treepruningwise.distFromRoot
Quartet concordance factors across Arabidopsis thalianaquartetCF
Binary trait simulationrbinTrait
Continuous trait simulationrTrait
Fits a population tree to data from quartet concordance factorsstepwise.test.tree
Tests the fit of a population tree to quartet concordance factor datatest.one.species.tree
data structure preparation for testing a population treetest.tree.preparation
Computations with a (generalized) three-point structured treethree.point.compute
Creates a tree with branch lengths to represent the 3-point structure of a covariance matrixtransf.branch.lengths