- There's no way to tell chisq.test the correct degrees of freedom ("df") - it cannot figure this out itself. My stats text tells me to reduce df by 1 for each value derived from the observations. If I have 10 buckets of counts AND I have calculated the mean and sd from the data, df = 7 NOT 9 as assumed by chisq.test().
- In the test distribution, again according to my text, no expected count should be less than 5. All the chisq.test does is tell you the results are unreliable - it doesn't fix them leaving the pre-processing up to you.
So here's how to use R's chisq.test()