R/bimac.R

In ouch: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

##' Anolis bimaculatus lizard size data
##'
##' This is the \emph{Anolis bimaculatus} dataset used in Butler & King (2004).
##' It is used to test a hypothesis of character displacement using an interspecific dataset of body sizes and current data on sympatry/allopatry.
##'
##' Explanations of the data follow:
##'   - **Body size.**
##'     We use the phenotypic data and phylogeny of Losos (1990), which employed the head lengths (of males) as a proxy for body size.
##'     In this group of lizards, head length correlates very strongly with snout-to-vent length and the cube root of mass, which are standard measures of body size.
##'     The data are head lengths in mm; note that we use the log of this value in analyses.
##'   - **Tree structure.**
##'     The phylogenetic tree is encoded via three variables:
##'     `node`, `ancestor`, and `time`.
##'     The `node` variable gives a name to each node.
##'     The `ancestor` variable names the ancestor of each node.
##'     The root node has no ancestor (i.e., \code{ancestor=NA}).
##'     The variable `time` specifies the temporal location of each node, the root node being at time 0.
##'   - **Specifications of selective regimes.**
##'     (Columns `OU.1`, `OU.3`, `OU.4`, `OU.LP`).
##'     These columns are factors, the levels of which correspond to the \dQuote{paintings} of the respective adaptive regime hypotheses onto the phylogeny (see [paint()]).
##'     Each selective regime is named (small, medium, large, etc.).
##'     Each column corresponds to a different painting of the selective regimes, and thus to a different hypothesis.
##'     In this example, there are 3 alternative models (see Butler & King 2004): `OU.4` is 4-regime model, `OU.3` is 3-regime model (all ancestors are medium), `OU.LP` is the linear parsimony model.
##'   - **Other variables.**
##'     In addition to the above, there is a two-letter code for each taxon (`spcode`) and the name of the island on which the taxon is found (`island`).
##'
##' @name bimac
##' @rdname bimac
##' @docType data
##' @family examples
##' @format A data frame with 45 observations on the following 11 variables.
##'    - `node`: Labels for the nodes.
##'    - `spcode`: Two-letter code for each taxon.
##'    - `species`: Species names for extant species.
##'    - `island`: Name of the island on which the population is found.
##'    - `size`: Body size (head length in mm) of extant species.
##'    - `ancestor`: Ancestral node.
##'    - `time`: Time of node.
##'    - `OU.1`: a factor with levels `ns`
##'    - `OU.3`: a factor with levels `small`, `medium`, `large`
##'    - `OU.4`: a factor with levels `small`, `medium`, `large`, `anc`
##'    - `OU.LP`: a factor with levels `small`, `medium`, `large`
##' @author Marguerite A. Butler and Aaron A. King
##' @references
##' \Lazell1972
##'
##' \Losos1990
##' @source \Butler2004
##' @keywords models
##' @example examples/bimac.R
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