I am trying to determine the best coding system for my categorical variables to use in a regression with categorical and continuous variables. I have been using this page as a resource but none of the coding methods seem to match what I want to do: http://www.ats.ucla.edu/stat/r/library/contrast_coding.htm
I have reason to expect that there could be differences among all four levels of a categorical variable and therefore would like to code it to perform all pairwise comparisons (1vs2, 1vs3, 1vs4, 2vs3, 2vs4, 3vs4,). I thought that a Sum (deviation) method would accomplish this as it says it compares each level to the grand mean. But in my model I only see terms for levels 1, 2, 3, and do not have a term for level 4 of the variable. Is this level incorporated into the intercept? If so is there another coding system I should use to get at the comparisons I am looking for?