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 <firstname.lastname@example.org>|
|License||GPL (>= 2) | file LICENSE|
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...