Solved – Alternative argument in Fisher’s exact test in R

fishers-exact-testhypothesis testingr

Can anyone please tell me what the alternative argument is in fisher.test() in R? What do greater and less imply?

fisher.test(x, y = NULL, workspace = 200000, hybrid = FALSE,
            control = list(), or = 1, alternative = "two.sided",
            conf.int = TRUE, conf.level = 0.95,
            simulate.p.value = FALSE, B = 2000)

I tried the help section and all it says is that alternative hypothesis must be one of "two.sided", "greater", or "less". When should I use each one? I'm looking at over-representation in my set against a control set.

Best Answer

This is the alternative hypothesis, commonly denoted by $H_1$. For example if you type or=1 and alternative=less, the $H_1$ hypothesis is $\psi<1$ where $\psi$ is the odds ratio (or).

Related Question