##### Code for ANCOVA in R


### Importing data


datum=read.csv(file.choose()) ### creates a data frame named datum from csv file

head(datum) ### column headers of data file plus first 6 rows of data 


###Plot Data

plot(Mass~Protein,data=datum) ### scatterplot of data used in example


### Run ANCOVA - treat Protein as continuous (linear) variable 

results=lm(Mass~Protein+Supplement,data=datum) ### linear regression of example data 
summary(results) ### prints a summary of 'results'
confint(results) ### Extract confidence intervals


### Run multi-factor ANOVA - treat Protein as categorical

results2=lm(Mass~as.factor(Protein)+Supplement,data=datum)
summary(results2)
TukeyHSD(results2)


anova(results2) ### generate an anova table of regression 
### BE VERY CAREFUL WITH THESE RESULTS - THEY ARE TYPE I SUM OF SQUARES

summary(aov(results2)) ### Also generates a type I sum of squares anova table


### Get type III sum of squares table
library(car)
Anova(results2,type=3)

### Note that there is no difference between type I and type III
### Sum of squares if model is fully factorial (no collinearity among variables)