How to interpret variable names/fixed effects in output (beginner question)


I am a beginner to R, RStudio, and any statistics really, but I have managed to do some analyses (Cox-models and Mixed linear models) that I am now trying to write up in summarizing tables for a report. In my output, the variables (e.g. "Breed" or "Treatment") get a number after it (e.g. "Breed1", "Breed2", "Treatment1" etc). How do I know which breed in my data frame "Breed1" refers to?

For each variable, the output also leaves out the numbers for one level. E.g. Breed3 is missing and Treatment2 as well. I feel like these should be included in my report - how do I get them?

Thanks in advance!

The second question is a statistics rather than an R question. If you have one set of fixed effects you can include all of them or include an intercept and all but one fixed effect. Why? The dummy variables add to one for all observations. The intercept corresponds to an independent variable equaling one. Including all the fixed effects and the intercept would be redundant--perfect multicollinearity.

When you have multiple fixed effects and an intercept, you need to leave out one category for each set of fixed effects. R is smart, and does this for you.

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