phylolm: Phylogenetic Linear Regression

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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
URLs

View on CRAN

Man pages

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...

Files in this package

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