MATLAB: What is the reference category for mnrfit when response variable is a categorical array

Question

I'm using mnrfit to estimate a binary logit model. The document says

Y can be one of the following:

• An n-by-k matrix, where Y(i,j) is the number of outcomes of the multinomial category j for the predictor combinations given by X(i,:). In this case, the number of observations are made at each predictor combination.
• An n-by-1 column vector of scalar integers from 1 to k indicating the value of the response for each observation. In this case, all sample sizes are 1.
• An n-by-1 categorical array indicating the nominal or ordinal value of the response for each observation. In this case, all sample sizes are 1.

and "The estimates for the kth category are taken to be zero as mnrfit takes the last category as the reference category". But if I have a categorical response variable (say H and L), how do I know which one MATLAB takes as the reference category without converting them to 1 and 2 first?

Answer 1

In general, the reference category will be the last category listed by "categories" function.

For example, in the first example in the "mnrfit" documentation, executing the following code:

>> cats=categories(sp)

results in:

cats = 
    'setosa'
    'versicolor'
    'virginica'

Here, the "mnrfit" function will use the last category in "cats" (in this case, "virginica") as the reference category.