R/anolis.R

In ouch: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

##' Greater Antillean anolis lizard sexual size dimorphism data
##'
##' The dataset consists of sexual size-dimorphism data for 38 species of anoles from Cuba, Hispaniola, Jamaica, and Puerto Rico (Butler, Schoener, and Losos 2000).
##' Each of these species belongs to one of six microhabitat types, or "ecomorphs" (sensu Williams, 1972):
##' trunk-ground, grass-bush, trunk, trunk-crown, twig, and crown-giant.
##' The data were used to demonstrate an evolutionary association between habitat type and degree of sexual size dimorphism.
##'
##' Size dimorphism was calcuated as the log-ratio of male snout-to-vent length to female snout-to-vent length (males are larger).
##'
##' In this example, we tested three models of evolution:
##' Brownian motion, Ornstein-Uhlenbeck with one global optimum, and Ornstein-Uhlenbeck with seven optima (one for each ecomorph type plus an additional one for an "unknown" type).
##'
##' For the seven-optima model, we assigned each terminal branch to an optimum according to the ecomorph type of the extant species.
##' Because we had no information to help guide hypotheses about internal branches, we assigned
##' internal branches to the "unknown" selective regime.
##' The phylogeny of these species is consistent with and adaptive radiation, with a burst of speciation events early in the evolutionary history of this clade (see phylogeny in Butler & King (2004) or example below).
##'
##' @name anolis.ssd
##' @rdname anolis_ssd
##' @family examples
##' @docType data
##' @format
##' A data frame with 38 observations on the following 6 variables.
##'   - `node`: Labels for the nodes.
##'   - `species`: Names of extant species.
##'   - `log.SSD`: Log sexual size dimorphism of extant species.
##'   - `ancestor`: Name of ancestor node.
##'   - `time`: Time of node.
##'   - `OU.1`: a factor with one level, `ns`.
##'   - `OU.7`: a factor with levels corresponding to ecomorph (`tg`, `tc`, `gb`, `cg`, `tw`, `tr`, `anc`).
##' @author Marguerite A. Butler, Aaron A. King
##' @references
##' \Butler2000
##'
##' \Williams1972
##'
##' @source \Butler2004
##' @keywords models
##' @example examples/anolis.R
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