##### Code for Conducting Post-hoc tests in R
 

### import data


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


### Run an ANOVA - must use AOV command to run some post-hoc tests


resultsAOV=aov(Mass~Season, data=datum)
summary(resultsAOV)


### Season is significant, so run a Tukey's post-hoc test

help(TukeyHSD)
TukeyHSD(resultsAOV) ### no 'summary', so no need to call is a object, just run the function TukeyHSD







##### Additional post-hoc tests - beyond scope of our class

library(emmeans)

results=lm(Mass~Season,data=datum)
summary(results)

#calculate estimated average of each group
Posthoc=emmeans(results,specs=~Season,CIs=TRUE) 
#CIs=TRUE means you want confidence intervals on averages
#plotit=FALSE means you don't want a plot


#calculate all pairwise comparisons
pairs(Posthoc)
#default uses TukeyHSD


pairs(Posthoc,adjust="bonferroni")
#bonferroni correction


#Other options:
#tukey - TukeyHSD
#scheffe
#sidak
#dunnettx
#mvt - multivariate t
#none