library(faraway) data(coagulation, package="faraway") coagulation plot(coag ~ diet, coagulation,ylab="coagulation time") stripchart(coag ~ diet, coagulation, vertical=TRUE, method="stack",xlab="diet",ylab="coagulation time") lmod <- lm(coag ~ diet, coagulation) sumary(lmod) round(coef(lmod),1) model.matrix(lmod) anova(lmod) lmodi <- lm(coag ~ diet -1, coagulation) sumary(lmodi) lmnull <- lm(coag ~ 1, coagulation) anova(lmnull,lmodi) options(contrasts=c("contr.sum","contr.poly")) lmods <- lm(coag ~ diet , coagulation) sumary(lmods) qqnorm(residuals(lmod)) qqline(residuals(lmod)) plot(jitter(fitted(lmod)),residuals(lmod),xlab="Fitted",ylab="Residuals") abline(h=0) med <- with(coagulation,tapply(coag,diet,median)) ar <- with(coagulation,abs(coag -med[diet])) anova(lm(ar ~ diet,coagulation)) bartlett.test(coag ~ diet, coagulation) 5 + c(-1,1) * qt(0.975, 24-4) * 1.53 se <- summary(lmod)$sigma 5 + c(-1,1) * qtukey(0.95, 4, 24-4)/sqrt(2) * se * sqrt(1/4 +1/6) (tci <- TukeyHSD(aov(coag ~ diet, coagulation))) plot(tci) data(jsp, package="faraway") jsp$mathcent <- jsp$math - mean(jsp$math) require(ggplot2) ggplot(aes(x=school,y=mathcent),data=jsp)+geom_boxplot() + theme(axis.text.x = element_text(angle = 90))+ylab("Centered Math Scores") lmod <- lm(mathcent ~ school-1, jsp) sumary(lmod) anova(lm(mathcent ~ school, jsp)) pvals <- summary(lmod)$coef[,4] padj <- p.adjust(pvals, method="bonferroni") coef(lmod)[padj < 0.05] names(which(sort(pvals) < (1:49)*0.05/49)) padj <- p.adjust(pvals, method="fdr") coef(lmod)[padj < 0.05]