To examine whether internalizing disorders loaded on one factor, and substance use factors loaded on another factor, we created two latent variables. Mood and anxiety disorders were loaded onto an internalizing psychopathology factor, and cannabis-use and alcohol-use disorders were loaded onto a substance use factor. The substance use and internalizing psychopathology factors were allowed to correlate. To identify our models, the loadings of the two substance use indicators were constrained to be equal. For this measurement model and all subsequent factor analyses, each diagnostic variable was regressed on its corresponding latent variable using probit regression assumptions. The variances of all latent factors were set to 1.0 to identify the models we tested.
