Model-based indices are calculated from the summation of model predictions of all sites i.e. the model-based time totals. Model predictions per site are based on the statistical model. Imputed values per site are observed values, plus, for missing counts, model predictions. Imputed indices are calculated from the imputed time totals.
Often, model-based indices and imputed indices hardly differ, and standard errors of imputed indices are expected to be close to the standard errors of model indices (see also the section in the TRIM manual on the equality of model-based and imputed indices). But model-based and imputed indices may differ. In favour of the use of model-based indices is that the indices might be somewhat more stable than imputed counts, especially if the model fits reasonably. In favour of imputed indices is that imputed indices stick close to the counts and may show a more realistic course in time, especially for linear trend models. We recommend to use imputed indices.