if(!require(nlme)){install.packages("nlme")} if(!require(multcomp)){install.packages("multcomp")} if(!require(multcompView)){install.packages("multcompView")} if(!require(lsmeans)){install.packages("lsmeans")} if(!require(lme4)){install.packages("lme4")} if(!require(lmerTest)){install.packages("lmerTest")} if(!require(TukeyC)){install.packages("TukeyC")} library(nlme) head(Cone11.11.1) names(Cone11.11.1)<-c("Site", "Habitat", "Individuals") model1=lme(Cone11.11.1$Individuals~Cone11.11.1$Site, random=~1|Cone11.11.1$Habitat, method="REML") anova.lme(model1, type="sequential", adjustSigma = FALSE) library(multcomp) posthoc1 =glht(model1, linfct=mcp(Site="Tukey")) mcs1=summary(posthoc1, test=adjusted("single-step")) mcs1 cld(mcs1, level=0.05, decreasing=TRUE) library(multcompView) library(lsmeans) lsm = lsmeans(model1, pairwise ~ Site, adjust="tukey") lsm cld(lsm, alpha=0.05, Letters=letters, adjust="tukey") model.fixed1 = gls (Individuals~Site, data=Cone11.11.1, method="REML") anova(model1, model.fixed1) library(ggplot2) ggplot(data=Cone11.11.1, aes(x=Site, y=Individuals))+geom_boxplot(aes(color=Habitat)) aov11.11.1<-aov(Individuals~Site*Habitat, data=Cone11.11.1) summary(aov11.11.1) TukeyHSD(aov11.11.1) barplot(Cone11.11.1$Individuals, col=c("yellow", "blue", "yellow", "blue", "yellow", "blue", "yellow", "blue", "yellow", "blue")) axis(side=1, at=c(0,1.2,3.6,6,8.4,10.8,12), labels=c(NA,"Site 1", "Site 2", "Site 3", "Site 4", "Site 5", NA), cex.lab = "2", cex.names = "2") legend("topright", c("Mangrove", "Sand"), fill=c("yellow", "blue"), box.lwd=0, y.intersp=1)