version 0.3-3

ChangeLog

@@ -1,3 +1,7 @@
+2006-01-04  Douglas Bates  <bates@stat.wisc.edu>
+
+	* man/BIB.Rd: Remove calls to gplot in this and other examples.
+
 2005-04-01  Douglas Bates  <bates@bates1-home>
 
 	* DESCRIPTION: Upgrade dependency to lme4_0.95-1 or later.  Change

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: SASmixed
-Version: 0.3-2
-Date: 2005-06-08
+Version: 0.3-3
+Date: 2006-01-05
 Title: Data sets from "SAS System for Mixed Models"
 Maintainer: Douglas Bates <bates@stat.wisc.edu>
 Author: Original by Littel, Milliken, Stroup, and Wolfinger
   modifications by Douglas Bates <bates@stat.wisc.edu>
 Description: Data sets and sample lme analyses corresponding
   to the examples in Littel, Milliken, Stroup and Wolfinger
   (1996), "SAS System for Mixed Models", SAS Institute.
-Depends: lme4 (>= 0.95-1)
-Suggests: latticeExtra
+Depends: Matrix (>= 0.99-1)
+Suggests: lattice
 LazyData: yes
 License: GPL version 2 or later
-Packaged: Wed Jun  8 11:27:06 2005; bates
+Packaged: Thu Jan  5 17:14:30 2006; bates

inst/doc/Usinglme.Rnw

@@ -16,8 +16,7 @@
   fontsize=\small}
 %%\VignetteIndexEntry{lmer for SAS PROC MIXED Users}
 %%\VignetteDepends{SASmixed}
-%%\VignetteDepends{lme4}
-%%\VignetteDepends{latticeExtra}
+%%\VignetteDepends{lattice}
 \begin{document}
 \SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=5,height=3,strip.white=TRUE}
 \SweaveOpts{prefix=TRUE,prefix.string=figs/f,include=FALSE}
@@ -30,12 +29,12 @@
 <<preliminaries,echo=FALSE,results=hide>>=
 options(width=75, contrasts=c(unordered="contr.SAS",ordered="contr.poly"))
 library(SASmixed)
-library(latticeExtra)
+library(lattice)
 @ 
 \section{Introduction}
 \label{sec:intro}
 
-The \code{lmer} function from the \code{lme4} library for \textsf{R} is used
+The \code{lmer} function from the \code{Matrix} library for \textsf{R} is used
 to fit linear mixed-effects models.  It is similar in scope to the
 \textsf{SAS} procedure \code{PROC MIXED} described in
 \citet{litt:mill:stro:wolf:1996}.
@@ -272,7 +271,10 @@ at the beginning of your session.
 \label{sec:AvgDailyGain}
 
 <<adg1,fig=TRUE,echo=TRUE,width=5,height=6>>=
-print(gplot(AvgDailyGain))
+print(xyplot(adg ~ Treatment | Block, AvgDailyGain, type = c("g", "p", "r"),
+       xlab = "Treatment (amount of feed additive)",
+       ylab = "Average daily weight gain (lb.)", aspect = "xy",
+       index.cond = function(x, y) coef(lm(y ~ x))[1]))
 @ 
 \begin{figure}[tbp]
   \centering
@@ -294,7 +296,9 @@ anova(fm2Adg)
 \section{BIB}
 \label{sec:BIB}
 <<bib1,fig=TRUE,echo=TRUE,width=6,height=6>>=
-print(gplot(BIB))
+print(xyplot(y ~ x | Block, BIB, groups = Treatment, type = c("g", "p"),
+             aspect = "xy", auto.key = list(points = TRUE, space = "right",
+             lines = FALSE)))
 @ 
 \begin{figure}[tbp]
   \centering

man/AvgDailyGain.Rd

@@ -39,13 +39,17 @@
 }
 \examples{
 options(contrasts = c(unordered = "contr.SAS", ordered = "contr.poly"))
-## plot of adg versus Treatment by Block
-if (require("latticeExtra", quietly = TRUE)) gplot(AvgDailyGain)
-fm1Adg <- lmer(adg ~ InitWt * Treatment - 1 + (1 | Block), AvgDailyGain)
-summary(fm1Adg) # compare with output 5.1, p. 178
+if (require("lattice", quietly = TRUE, character = TRUE)) {
+  ## plot of adg versus Treatment by Block
+  xyplot(adg ~ Treatment | Block, AvgDailyGain, type = c("g", "p", "r"),
+         xlab = "Treatment (amount of feed additive)",
+         ylab = "Average daily weight gain (lb.)", aspect = "xy",
+         index.cond = function(x, y) coef(lm(y ~ x))[1])
+}
+# compare with output 5.1, p. 178
+(fm1Adg <- lmer(adg ~ InitWt * Treatment - 1 + (1 | Block), AvgDailyGain))
 anova(fm1Adg)   # checking significance of terms
-fm2Adg <- lmer(adg ~ InitWt + Treatment + (1 | Block), AvgDailyGain)
-summary(fm2Adg)
+(fm2Adg <- lmer(adg ~ InitWt + Treatment + (1 | Block), AvgDailyGain))
 anova(fm2Adg)
 summary(lmer(adg ~ InitWt + Treatment - 1 + (1 | Block), AvgDailyGain))
 }

man/BIB.Rd

@@ -38,7 +38,11 @@
 }
 \examples{
 options(contrasts = c(unordered = "contr.SAS", ordered = "contr.poly"))
-if (require("latticeExtra", quietly = TRUE)) gplot(BIB)
+if (require("lattice", quietly = TRUE, character = TRUE)) {
+  xyplot(y ~ x | Block, BIB, groups = Treatment, type = c("g", "p"),
+         aspect = "xy", auto.key = list(points = TRUE, space = "right",
+         lines = FALSE))
+}
 fm1BIB <- lmer(y ~ Treatment * x + (1 | Block), BIB)
 summary(fm1BIB)   # compare with Output 5.7, p. 188
 anova(fm1BIB)     # strong evidence of different slopes

man/HR.Rd

@@ -34,7 +34,11 @@
 }
 \examples{
 options(contrasts = c(unordered = "contr.SAS", ordered = "contr.poly"))
-if (require("latticeExtra", quietly = TRUE)) gplot(HR)
+if (require("lattice", quietly = TRUE, character = TRUE)) {
+  xyplot(HR ~ Time | Patient, HR, type = c("g", "p", "r"), aspect = "xy",
+         index.cond = function(x, y) coef(lm(y ~ x))[1],
+         ylab = "Heart rate (beats/min)")
+}
 (fm1HR <- lmer(HR ~ Time * Drug + baseHR + (Time|Patient), HR))  # linear trend in time
 anova(fm1HR)
 \dontrun{