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Is it acceptable (publishable) to run a multilevel model with only level-2 and level-3 predictors? Example: Looking only at the effect of school resources, size or location, and at the district level (budget etc.). The dataset does not contain individual level variables (e.g. gender, SES etc.)

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Yes, it's acceptable. Sometimes you don't have level 1 predictors. If you don't have them, you can't use them.

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