Instruments for the level model must be uncorrelated with the unobserved group-specific effects, no matter whether you specify them with gmmiv() or iv(). Without option diff, this requires that the levels of those instruments themselves are uncorrelated with those unobserved effects, which is akin to a "random-effects" assumption. With option diff, the first-differenced instruments need to be uncorrelated with the unobserved effects, which is a weaker requirement but still needs to be justified (see the seminal paper by Blundell and Bond (1998)).
Sarah Magd
This topic is about the xtdpdgmm command. It would be better to start a different topic if you have a question about a different command, such as xtabond2. Some general comments:
- System GMM requires stronger assumptions about the initial observations than difference GMM. In a macroeconomic context, the additional assumption is quite likely to be violated due to the heterogeneous development of the countries. Unfortunately, in the empirical practice there is often not much effort made in justifying the extra assumption for system GMM. Just because the relevant literature used system GMM, this does not mean that it really is justified.
- If there is a lot of persistence in the data, which again is quite likely with macroeconomic data, then difference GMM might suffer from a weak-instruments problem and the coefficient of the lagged dependent variable can be severely downward biased. This would be consistent with the difference in estimates between the difference and system GMM estimator, but the first point above could also explain that difference if the additional assumption for system GMM is violated. Also, even if both estimators are consistent, in small samples they can have a large sampling variation, which could lead to the different estimates you observed.
- If the true data-generating process is dynamic, then estimating a static fixed-effects model yields biased estimates. So, it could be coincidentally that the bias from the static fixed-effects estimator is similar to the bias of the difference GMM estimator.
- In order to reduce the weak-instruments problem of the difference GMM estimator, without imposing the stronger assumption for system GMM, a good solution can be to use the difference GMM estimator with added nonlinear moment conditions; see xtdpdgmm option nl(noserial).

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