[Lme4-commits] r1615 - in pkg/lme4Eigen: data man

[noreply at r-forge.r-project.org]

Author: bbolker
Date: 2012-02-23 23:06:24 +0100 (Thu, 23 Feb 2012)
New Revision: 1615

Added:
   pkg/lme4Eigen/data/grouseticks.rda
   pkg/lme4Eigen/man/grouseticks.Rd
Log:

  add grouse tick data



Added: pkg/lme4Eigen/data/grouseticks.rda
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Property changes on: pkg/lme4Eigen/data/grouseticks.rda
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Added: svn:mime-type
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Added: pkg/lme4Eigen/man/grouseticks.Rd
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--- pkg/lme4Eigen/man/grouseticks.Rd	                        (rev 0)
+++ pkg/lme4Eigen/man/grouseticks.Rd	2012-02-23 22:06:24 UTC (rev 1615)
@@ -0,0 +1,64 @@
+\name{grouseticks}
+\alias{grouseticks}
+\alias{grouseticks_agg}
+\docType{data}
+\title{
+  Data on red grouse ticks from Elston et al. 2001
+}
+\description{
+  Number of ticks on the heads of red grouse chicks
+  sampled in the field (\code{grouseticks})
+  and an aggregated version (\code{grouseticks_agg}); see original source for more details
+}
+\usage{data(grouseticks)}
+\format{
+  \describe{
+    \item{\code{INDEX}}{(factor) chick number (observation level)}
+    \item{\code{TICKS}}{number of ticks sampled}
+    \item{\code{BROOD}}{(factor) brood number}
+    \item{\code{HEIGHT}}{height above sea level (meters)}
+    \item{\code{YEAR}}{year (-1900)}
+    \item{\code{LOCATION}}{(factor) geographic location code}
+    \item{\code{cHEIGHT}}{centered height, derived from \code{HEIGHT}}
+    \item{\code{meanTICKS}}{mean number of ticks by brood}
+    \item{\code{varTICKS}}{variance of number of ticks by brood}
+  }
+}
+\source{
+  Robert Moss, via David Elston
+}
+\details{\code{grouseticks_agg} is just a brood-level
+  aggregation of the data}
+\references{
+  Elston, D. A., R. Moss, T. Boulinier, C. Arrowsmith, and
+X. Lambin. 2001. "Analysis of Aggregation, a Worked Example: Numbers of
+Ticks on Red Grouse Chicks." Parasitology 122 (05):
+563-569. doi:10.1017/S0031182001007740.
+\url{http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=82701}.
+}
+\examples{
+data(grouseticks)
+## Figure 1a from Elston et al
+par(las=1,bty="l")
+tvec <- c(0,1,2,5,20,40,80)
+pvec <- c(4,1,3)
+with(grouseticks_agg,plot(1+meanTICKS~HEIGHT,
+                  pch=pvec[factor(YEAR)],
+                  log="y",axes=FALSE,
+                  xlab="Altitude (m)",
+                  ylab="Brood mean ticks"))
+axis(side=1)
+axis(side=2,at=tvec+1,label=tvec)
+box()
+abline(v=405,lty=2)
+## Figure 1b
+with(grouseticks_agg,plot(varTICKS~meanTICKS,
+                  pch=4,
+                  xlab="Brood mean ticks",
+                  ylab="Within-brood variance"))
+curve(1*x,from=0,to=70,add=TRUE)
+## Model fitting
+form <- TICKS~YEAR+HEIGHT+(1|BROOD)+(1|INDEX)+(1|LOCATION)
+(full_mod1  <- glmer(form, family="poisson",data=grouseticks))
+}
+\keyword{datasets}