Blanks
Blank values in the data are inherently ambiguous. Some people use blanks as a shorthand notation for values of 0, particularly in occurrence seriation where the values would normally be 0 and 1. For simplicity's sake only the 1's are entered in the data matrix. At other times blanks are supposed to indicate a feature is missing or absent for an artifact (for example, the feature might be the color of an ornamental band on pottery and the feature might be absent on some artifacts). Alternatively, a blank could signify the absence of data rather than the absence of the feature - we simply don't know anything about this feature for this artifact. Whatever convention you are using, you need to let OptiPath know by setting the feature parameter Blanks.
Blanks can be interpreted in three different ways: as unknowns, as absences or as zeroes. When choosing a value for Blanks, the options are Unknown, Absent and Zero.
If the feature parameter Blanks is set to Unknown, blanks are taken to mean that the true value of the feature for the artifact is unknown and the feature will have no effect in the computation of distance between artifacts. This means this feature's contribution to the distance, including any transition penalty, is zero.
If the feature parameter Blanks is set to Absent, blanks are treated like absences and will affect the computation of transition penalties but otherwise they are treated like unknown values and have no effect in computing distance between artifacts.
If the feature parameter Blanks is set to Zero, blanks will be interpreted according to the setting for the feature parameter Zeroes.
Blanks can indicate that the feature value is unknown, that the feature is absent or that it has a value of zero. You may indicate that blanks should be assumed to indicate both a value of zero and an absence (for example, when a feature is the width of an ornamental band on pottery) by telling OptiPath to interpret a blank as a value of zero and to interpret zeroes as both a value and an absence (see Zeroes).
Each setting for Blanks can lead to different results in seriation. For more information see Setting the Earlier, Later, Blanks, Zeroes and Transition Parameters.