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The best analysis is that which allows the IFS models  to subsequently produce forecasts that verify nearest to the actual evolution.  The analysis is not necessarily true to the observations in every respect, though of course the analysis processes (4D-Var and LDAS) try to assimilate them to best effect.  For the purposes of the ensemble, the analysis process also tries to quantify the uncertainty of our estimate of the initial state.  Advanced analysis procedures have to be used to assimilate non-conventional observations. 

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Users need to be aware of potential problems with the forecast due to deficiencies in coverage of data or conflict of observations with background fields.  Users should inspect:

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