https://github.com/cran/aster
Tip revision: aa47935123bfca8a22cbc8345d658d0c1713a289 authored by Charles J. Geyer on 14 December 2023, 15:20:02 UTC
version 1.1-3
version 1.1-3
Tip revision: aa47935
radish.Rd
\name{radish}
\docType{data}
\alias{radish}
\title{Life History Data on Raphanus sativus}
\description{
Data on life history traits for the
invasive California wild radish \emph{Raphanus sativus}
}
\usage{data(radish)}
\format{
A data frame with records for 286 plants.
Data are already in \dQuote{long} format; no need to reshape.
\describe{
\item{resp}{Response vector.}
\item{varb}{Categorical. Gives node of graphical model corresponding
to each component of \code{resp}. See details below.}
\item{root}{All ones. Root variables for graphical model.}
\item{id}{Categorical. Indicates individual plants.}
\item{Site}{Categorical. Experimental site where plant was grown.
Two sites in this dataset.}
\item{Block}{Categorical. Block nested within site.}
\item{Region}{Categorical. Region from which individuals
were obtained: northern, coastal California (N) or southern, inland
California (S).}
\item{Pop}{Categorical. Wild population nested within region.}
\item{varbFlowering}{Indicator (zero or one). Shorthand
for \code{as.numeric(radish$varb == "Flowering")}.}
\item{varbFlowers}{Indicator (zero or one). Shorthand
for \code{as.numeric(radish$varb == "Flowers")}.}
\item{fit}{Indicator (zero or one). Shorthand
for \code{as.numeric(radish$varb == "Fruits")}. So-called because the
components of \code{outcome} indicated are the best surrogate of
Darwinian fitness in these data.}
}
}
\details{
The levels of \code{varb} indicate nodes of the graphical model to which
the corresponding elements of the response vector \code{resp} belong.
This is the typical \dQuote{long} format produced by the R \code{reshape}
function. For each individual, there are several response variables.
All response variables are combined in one vector \code{resp}.
The variable \code{varb} indicates which \dQuote{original} variable
the number was for. The variable \code{id} indicates which individual
the number was for. The levels of \code{varb}, which are the names
of the \dQuote{original} variables are
\describe{
\item{Flowering}{Indicator (zero or one). Bernoulli, One if individual
survived to produce flowers.}
\item{Flowers}{Integer. Zero-truncated Poisson, number of flowers observed.}
\item{Fruits}{Integer. Poisson, number of fruits observed.}
}
Graphical model is
\deqn{1 \longrightarrow \mbox{Flowering} \longrightarrow \mbox{Flowers} \longrightarrow \mbox{Fruits}}{1 -> Flowering -> Flowers -> Fruits.}
}
\source{
Caroline Ridley
}
\references{
These data are a subset of data previously analyzed using fixed effect
aster methods (R function \code{aster}) in the following.
Ridley, C. E. and Ellstrand, N. C. (2010).
Rapid evolution of morphology and adaptive life history in
the invasive California wild radish (\emph{Raphanus sativus}) and
the implications for management.
\emph{Evolutionary Applications}, \bold{3}, 64--76.
These data are a subset of data previously analyzed using random effect
aster methods (R function \code{reaster}) in the following.
Geyer, C. J., Ridley, C. E., Latta, R. G., Etterson, J. R.,
and Shaw, R. G. (2013)
Local Adaptation and Genetic Effects on Fitness: Calculations
for Exponential Family Models with Random Effects.
\emph{Annals of Applied Statistics}, \bold{7}, 1778--1795.
\doi{10.1214/13-AOAS653}.
}
\seealso{
\code{\link{pickle}}
}
\examples{
data(radish)
}
\keyword{datasets}