###Lecture 28 - Code for running an ANOVA and Post-hoc tests (Tukey's HSD) in R

### import data

datum=read.csv(file.choose())
head(datum)

### Run the Analysis 

results=lm(Y~X,data=datum) ### Run an ANOVA using the general linear model
### Note: replace 'Y' in above statement with Y variable
### Replace 'X' in above statement with X variable

### NOTE THAT LM DOES NOT MAINTAIN THE EXPERIMENT-WISE ERROR RATE!


### Run the Post-Hoc Tests

### NOTE THAT TUKEY'S CODE WILL NOT WORK ON AN LM, ONLY AOV
results2=aov(results) ### convert results 2 (lm) to an true ANOVA

TukeyHSD(results2) ### Run a TukeyHSD PostHoc test on results

###diff is difference between specified groups
###lwr is lower confidence limit on difference
###upr is upper confidence limit on difference
###subtract diff from upr to get confidence interval
###p adj is p-value for null hypothesis of no difference between the two specified groups

###Note that 'diff' from results2 are same as beta from results.
###Tukey's only adjusts p-values and confindence intervals, not betas.


### Plot results

plot(datum$X,datum$Y)
### Note: replace 'Y' in above statement with Y variable
### Replace 'X' in above statement with X variable