The study protocol will have specified the questions to be addressed by the study and will contain a generic description of the study design and the statistical methods. However, the SAP is likely to be the document in which the statistics to be calculated, and tabular and graphical presentations, are fully described. It provides a more detailed elaboration of the statistical modelling of outcomes, plans for measuring the outcomes and predictor variables, whether there will be control variables, confidence intervals, multiplicity issues and how missing data will be handled (for handling of missing data, see Chapter 6.3). Since the decision criteria for the study are specified in terms of the observed values of these detailed statistics, it is worth formulating the SAP at an early stage and, in particular, before any informal inspection of aspects of the data or results that might influence opinions regarding the study hypotheses. Ideally the SAP will be developed as soon as the protocol is finalised.
A particular concern in retrospective studies is that decisions about the analysis should be made blinded to any knowledge of the results. This should be a consideration in the study design, particularly when feasibility studies are to be performed to inform the design phase. Feasibility studies should be independent of the main study results (see Chapter 2).
At any cost, a SAP should always be completed before the data have been unblinded for the statistician. This contributes to the transparency of the study and that the set of analyses have not been influenced by the data. Making alterations to a planned statistical analysis after seeing the data increases the risk of bias and inflates the probability of type I errors.