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I just wondered if there was a way of stopping MLwiN from setting residuals which are too close to zero to be missing values? I know this can be done through the command interface using MISR 0 if using MLwiN directly but is there runmlwin code which will do this as well?

You can specify this with the norecode option within the residual sub-options (for details of this and other settings see help runmlwin within Stata)

Thx. Hello Neighbor