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@@ -16,6 +16,7 @@ lib | |
| library | ||
| check | ||
| www | ||
| examples | ||
| ^(.+?)\.tar\.gz | ||
| ^(.+?)\.tgz | ||
|
|
||
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| @@ -1,21 +1,32 @@ | ||
| useDynLib(ouch,.registration=TRUE) | ||
| # Generated by roxygen2: do not edit by hand | ||
|
|
||
| export(ape2ouch) | ||
| export(brown) | ||
| export(hansen) | ||
| export(ouchtree) | ||
| export(paint) | ||
| exportMethods(bootstrap) | ||
| exportMethods(coef) | ||
| exportMethods(logLik) | ||
| exportMethods(plot) | ||
| exportMethods(print) | ||
| exportMethods(show) | ||
| exportMethods(simulate) | ||
| exportMethods(summary) | ||
| exportMethods(update) | ||
| import(methods) | ||
| importFrom(subplex,subplex) | ||
| importFrom(stats,deviance,simulate,update,coef,logLik,optim, | ||
| rnorm,runif,setNames) | ||
| importFrom(utils,head,tail) | ||
| importFrom(graphics,plot,par,text) | ||
| importFrom(grDevices,rainbow) | ||
| exportClasses('ouchtree','browntree','hansentree') | ||
| exportMethods( | ||
| 'plot','logLik','summary','coef','coerce', | ||
| 'print','show', | ||
| 'simulate','update','bootstrap' | ||
| ) | ||
| export( | ||
| ouchtree, | ||
| brown, | ||
| hansen, | ||
| ape2ouch, | ||
| paint | ||
| ) | ||
| importFrom(graphics,par) | ||
| importFrom(graphics,text) | ||
| importFrom(stats,coef) | ||
| importFrom(stats,logLik) | ||
| importFrom(stats,optim) | ||
| importFrom(stats,rnorm) | ||
| importFrom(stats,runif) | ||
| importFrom(stats,setNames) | ||
| importFrom(stats,simulate) | ||
| importFrom(stats,update) | ||
| importFrom(subplex,subplex) | ||
| importFrom(utils,head) | ||
| importFrom(utils,tail) | ||
| useDynLib(ouch, .registration = TRUE) |
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| #' 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 \dQuote{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 7 optima (one for each ecomorph type plus an additional one for an \dQuote{unknown} type). | ||
| #' | ||
| #' For the 7-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 \dQuote{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 | ||
| #' @docType data | ||
| #' @format | ||
| #' A data frame with 38 observations on the following 6 variables. | ||
| #' \describe{ | ||
| #' \item{node}{Labels for the nodes.} | ||
| #' \item{species}{Names of extant species.} | ||
| #' \item{log.SSD}{Log sexual size dimorphism of extant species.} | ||
| #' \item{ancestor}{Ancestor node.} | ||
| #' \item{time}{Time of node.} | ||
| #' \item{OU.1}{a factor with levels \code{ns}} | ||
| #' \item{OU.7}{a factor with levels corresponding to ecomorph | ||
| #' (\code{tg} \code{tc} \code{gb} \code{cg} \code{tw} \code{tr} \code{anc})} | ||
| #' } | ||
| #' @author Marguerite A. Butler, Aaron A. King | ||
| #' @references | ||
| #' \Butler2000 | ||
| #' | ||
| #' \Williams1972 | ||
| #' | ||
| #' @source \Butler2004 | ||
| #' @keywords models | ||
| #' @example examples/anolis.R | ||
| #' | ||
| NULL |
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| Original file line number | Diff line number | Diff line change |
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| #' 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. | ||
| #' The data frame has the following columns: | ||
| #' \code{species} which are species names, | ||
| #' \code{size} which is the phenotypic data, | ||
| #' and the variables \code{ancestor} and \code{time} which specify the topology of the phylogeny and the location of the nodes in time, respectively. | ||
| #' The columns \code{OU.1}, \code{OU.3}, \code{OU.4}, and \code{OU.LP} specify four hypothetical arrangements of selective regimes. | ||
| #' Explanations of the data follow: | ||
| #' \describe{ | ||
| #' \item{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. | ||
| #' } | ||
| #' \item{Tree topology}{ | ||
| #' The tree topology is encoded via two vectors: \code{ancestor} and \code{time}. | ||
| #' Each node of the' phylogenetic tree has a corresponding row in the data frame, numbered from 1 to 45. | ||
| #' The columns \code{ancestor} and \code{time} specify the phylogeny. | ||
| #' The \code{ancestor} variable specifies the topology: it is a list indicating the ancestor of each node. | ||
| #' The root node has ancestor 0. | ||
| #' The variable \code{time} specifies the temporal location of each node, with the root node being at time 0. | ||
| #' } | ||
| #' \item{Specifications of selective regimes.}{ | ||
| #' (Columns \code{OU.1}, \code{OU.3}, \code{OU.4}, \code{OU.LP}). | ||
| #' These columns are factors, the levels of which correspond to the \dQuote{paintings} of the respective adaptive regime hypotheses onto the phylogeny. | ||
| #' 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): \code{OU.4} is 4-regime model, \code{OU.3} is 3-regime model (all ancestors are medium), \code{OU.LP} is the linear parsimony model. | ||
| #' } | ||
| #' } | ||
| #' | ||
| #' @name bimac | ||
| #' @docType data | ||
| #' @format A data frame with 45 observations on the following 8 variables. | ||
| #' \describe{ | ||
| #' \item{node}{Labels for the nodes.} | ||
| #' \item{species}{Species names for extant species.} | ||
| #' \item{size}{Body size (head length in mm) of extant species.} | ||
| #' \item{ancestor}{Ancestral node.} | ||
| #' \item{time}{Time of node.} | ||
| #' \item{OU.1}{a factor with levels \code{ns}} | ||
| #' \item{OU.3}{a factor with levels \code{small}, \code{medium}, \code{large}} | ||
| #' \item{OU.4}{a factor with levels \code{small}, \code{medium}, \code{large}, \code{anc}} | ||
| #' \item{OU.LP}{a factor with levels \code{small}, \code{medium}, \code{large}} | ||
| #' } | ||
| #' @author Marguerite A. Butler and Aaron A. King | ||
| #' @references | ||
| #' \Lazell1972 | ||
| #' | ||
| #' \Losos1990 | ||
| #' @source \Butler2004 | ||
| #' @keywords models | ||
| #' @example examples/bimac.R | ||
| #' | ||
| NULL |
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