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phylolm: R package for Phylogenetic Linear Regression on very large trees

The package provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. Computations use 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. When a new version is stable, it is pushed to CRAN, so the version available here is newer than that on CRAN.

  • Lam Si Tung Ho and Cécile Ané (2014).

Intrinsic inference difficulties for trait evolution with Ornstein-Uhlenbeck models. Methods in Ecology and Evolution 5(11):1133-1146. (link)

  • Lam Si Tung Ho and Cécile Ané (2014).

A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Systematic Biology 63(3):397-408. (link to pdf)

Installation

Install phylolm from github:

devtools::install_github("lamho86/phylolm")

Main features

  • phylogenetic signal
  • phylogenetic linear, logistic and Poisson regression
  • stepwise model selection (from v2.3)
  • OU shift detection
  • continuous and discrete trait simulators with covariates
  • bootstrap-based confidence intervals for phylogenetic logistic regression (from v2.3) and phylogenetic regression (from v2.4.2)
  • goodness-of-fit test of a population tree with the coalescent (from v.2.4)
  • allowing measurement errors in phylogenetic linear regression (from v2.4.1)
  • log likelihood of an one-dimensional Ornstein-Uhlenbeck model (from v2.5)
  • bootstrapping can be parallelized (from v2.6)
  • R-squared and Adjusted R-squared (from v2.6.1)
  • phyloglmstep (from v2.6.2)
  • mace (from v2.6.4)
  • REML for phylolm (from v2.6.4)
  • Compatible with visreg (from v2.6.5)

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Version

Install

install.packages('phylolm')

Monthly Downloads

4,020

Version

2.6.5

License

GPL (>= 2) | file LICENSE

Issues

11

Pull Requests

2

Stars

30

Forks

13

Maintainer

Lam Si Tung Ho

Last Published

September 30th, 2024

Functions in phylolm (2.6.5)

phyloglm

Phylogenetic Generalized Linear Model
guidetree

Binary population tree within Arabidopsis thaliana
OUshifts-methods

Methods for class 'OUshifts'.
phylolm-methods

Methods for class 'phylolm'.
mace

Multi-task learning for ancestral state estimation.
phylolm-package

Phylogenetic Linear Regression
OUshifts

Detections of shifts in the OU process along a phylogeny.
phyloglm-methods

Methods for class 'phyloglm'.
phylolm

Phylogenetic Linear Model
test.one.species.tree

Tests the fit of a population tree to quartet concordance factor data
phyloglmstep

Stepwise model selection for Phylogenetic Generalized Linear Model
pruningwise.distFromRoot

Calculates node distance from the root in an "pruningwise" tree
test.tree.preparation

data structure preparation for testing a population tree
pruningwise.branching.times

Calculates internal node ages in an ultrametric "pruningwise" tree
flowerSize

Flower size of 25 Euphorbiaceae species
phylostep

Stepwise model selection for Phylogenetic Linear Model
rbinTrait

Binary trait simulation
stepwise.test.tree

Fits a population tree to data from quartet concordance factors
quartetCF

Quartet concordance factors across Arabidopsis thaliana
three.point.compute

Computations with a (generalized) three-point structured tree
transf.branch.lengths

Creates a tree with branch lengths to represent the 3-point structure of a covariance matrix
rTrait

Continuous trait simulation
OU1d.loglik

Log likelihood of an one-dimensional Ornstein-Uhlenbeck model
flowerTree

Phylogenetic tree of 25 Euphorbiaceae species