I am trying to analyse variance of difference between pH values measures by two different methods. I have repeated measurements from a number of subjects and I want to analyse within subject variance and between subject variance, but when I use the
aov() function in R degrees of freedom seems to be incorrect.
My dataset looks like this:
id <- c(1,1,1,2,2,3,3,3,3,6,6,6,8,8,9,9,9,9) ph1 <- c(7,6,6,8,8,8,4,3,5,6,6,7,8,8,5,4,3,6) # This is the gold standard method. ph2 <- c(8,6,7,8,7,8,5,4,5,6,6,7,8,9,4,3,4,6) df <- as.data.frame(cbind(id,ph1,ph2))
And when I calculate one-way ANOVA I get this:
res.aov <- aov((ph1-ph2) ~ id, data = df) summary(res.aov) Df Sum Sq Mean Sq F value Pr(>F) id 1 0.579 0.5792 1.17 0.295 Residuals 16 7.921 0.4950
Should Df for between groups analysis be 5 or have I misunderstod something?