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.

Author | Lam Si Tung Ho [aut, cre], Cecile Ane [aut], Robert Lachlan [ctb], Kelsey Tarpinian [ctb], Rachel Feldman [ctb], Qing Yu [ctb] |

Date of publication | 2016-10-17 19:00:05 |

Maintainer | Lam Si Tung Ho <lamho86@gmail.com> |

License | GPL (>= 2) | file LICENSE |

Version | 2.5 |

https://CRAN.R-project.org/package=phylolm |

**flowerSize:** Flower size of 25 Euphorbiaceae species

**flowerTree:** Phylogenetic tree of 25 Euphorbiaceae species

**guidetree:** Binary population tree within Arabidopsis thaliana

**OU1d.loglik:** Log likelihood of an one-dimensional Ornstein-Uhlenbeck model

**OUshifts:** Detections of shifts in the OU process along a phylogeny.

**OUshifts-methods:** Methods for class 'OUshifts'.

**phyloglm:** Phylogenetic Generalized Linear Model

**phyloglm-methods:** Methods for class 'phyloglm'.

**phylolm:** Phylogenetic Linear Model

**phylolm-methods:** Methods for class 'phylolm'.

**phylolm-package:** Phylogenetic Linear Regression

**phylostep:** Stepwise model selection for Phylogenetic Linear Model

**pruningwise.branching.times:** Calculates internal node ages in an ultrametric "pruningwise"...

**pruningwise.distFromRoot:** Calculates node distance from the root in an "pruningwise"...

**quartetCF:** Quartet concordance factors across Arabidopsis thaliana

**rbinTrait:** Binary trait simulation

**rTrait:** Continuous trait simulation

**stepwise.test.tree:** Fits a population tree to data from quartet concordance...

**test.one.species.tree:** Tests the fit of a population tree to quartet concordance...

**test.tree.preparation:** data structure preparation for testing a population tree

**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...

phylolm

phylolm/inst

phylolm/inst/CITATION

phylolm/tests

phylolm/tests/testthat.R

phylolm/tests/testthat

phylolm/tests/testthat/testOU1d.R

phylolm/src

phylolm/src/Makevars

phylolm/src/threepoint.c

phylolm/src/transbranchlengths.c

phylolm/src/logistreglikelihood.c

phylolm/src/phylolm.h

phylolm/NAMESPACE

phylolm/data

phylolm/data/quartetCF.rda

phylolm/data/guidetree.rda

phylolm/data/flowerSize.rda

phylolm/data/flowerTree.rda

phylolm/R

phylolm/R/OUshifts.R
phylolm/R/phylolm.R
phylolm/R/phyloglm.R
phylolm/R/OU1d.R
phylolm/R/rTrait.R
phylolm/R/tools.R
phylolm/R/phylostep.R
phylolm/R/rbinTrait.R
phylolm/R/testingTreeWithQuartetCF.r

phylolm/README.md

phylolm/MD5

phylolm/DESCRIPTION

phylolm/man

phylolm/man/rbinTrait.Rd
phylolm/man/flowerSize.Rd
phylolm/man/transf.branch.lengths.Rd
phylolm/man/OUshifts-methods.Rd
phylolm/man/phylolm-package.Rd
phylolm/man/OUshifts.Rd
phylolm/man/phylostep.Rd
phylolm/man/flowerTree.Rd
phylolm/man/phylolm-methods.Rd
phylolm/man/guidetree.Rd
phylolm/man/quartetCF.Rd
phylolm/man/phyloglm-methods.Rd
phylolm/man/stepwise.test.tree.Rd
phylolm/man/OU1d.loglik.Rd
phylolm/man/test.tree.preparation.Rd
phylolm/man/pruningwise.branching.times.Rd
phylolm/man/rTrait.Rd
phylolm/man/phyloglm.Rd
phylolm/man/phylolm.Rd
phylolm/man/test.one.species.tree.Rd
phylolm/man/pruningwise.distFromRoot.Rd
phylolm/man/three.point.compute.Rd
phylolm/LICENSE

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