#10.1
numSummary (ellisyuan$syntaxvariety, groups=ellisyuan$group, statistics=c("mean", "sd"))

#10.1.1 Boxplots with Overlaid Dotcharts
##Step1
bx.p<-boxplot(syntaxvariety~group, data=ellisyuan)
## boxplot(syntaxvariety~group, data=ellisyuan)
##Step2 
with (ellisyuan,
{bxp (bx.p, staplewex=1, boxfill="light grey", medlwd=8, medcol="white",
boxwex=.5, ylab="Syntactic variety", outl=F)
points (jitter (rep (1:3, each=14), 1.2),
unlist (split (syntaxvariety, group)),
cex=.8, pch=16)})




AnovaModel.1 <- aov(syntaxvariety~group, data=ellisyuan)

summary(AnovaModel.1)

Anova(AnovaModel.1, type=c('II'))

oneway.test(syntaxvariety~group, data=ellisyuan, var.equal=T)

leveneTest(ellisyuan$syntaxvariety, ellisyuan$group)

numSummary(ellisyuan$syntaxvariety , groups=ellisyuan$group, statistics=c("mean", "sd"))




install.packages("multcomp")
library(multcomp)
.Pairs <- glht(AnovaModel.1, linfct=mcp(group="Tukey"))
.Pairs
confint(.Pairs) 
plot(confint(.Pairs))

summary(.Pairs,adjusted(type=c(p.adjust.methods=c("fdr"))))

plot(confint(.Pairs))




library(HH)
ellisyuan.mmc <- mmc(AnovaModel.1, linfict=mcp(group="Tukey", interaction_average=TRUE))
mmcplot(ellisyuan.mmc)


##10.3.1
levels(ellisyuan$group) #find out names
levels(ellisyuan$group)=c("NP","PTP","OLP") #set new names
levels(ellisyuan$group)
contr=rbind("NP-PTP"=c(1,-1,0), "NP-OLP"=c(1,0,1), "PTP-OLP"=c(0,1,-1))
contr
Ellisyuan.Pairs=glht(AnovaModel.1, linfct=mcp(group=contr))
Ellisyuan.Pairs

#10.4
ellisyuan.anova <- aov(words~group, data=ellisyuan)
ellisyuan.anova
ellisyuan.Pairs <- glht(ellisyuan.anova, linfct=mcp(group="Tukey"))
ellisyuan.Pairs
summary(ellisyuan.Pairs)

install.packages(c("MASS", "akima", "robustbase"))
install.packages(c("cobs", "robust", "mgcv", "scatterplot3d", "quantreg", "rrcov", "lars", "pwr", "trimcluster", "parallel", "mc2d", "psych", "Rfit"))
install.packages("WRS", repos="http://R-Forge.R-project.org", type="source")
library(WRS)
ellis=list()
ellis[[1]]=subset(ellisyuan, subset=group=="NP", select=c(words))
ellis[[2]] <- subset(ellisyuan, subset=group=="PTP", select=c(words))
ellis[[3]] <- subset(ellisyuan, subset=group=="OLP", select=c(words))
t1waybt(ellis, tr=.2, nboot=599)


mcppb20(ellis)
mcppb20(ellis, crit=NA, con=0, tr=.2, alpha=.05, nboot=2000, grp=NA)

#10.5 Application (pp.202-204)