Occurrence Seriation
Occurrence seriation is the ordering or arrangement of items (artifacts) according to the presence or absence of their constituent features (practitioners of occurrence seriation often refer to a "class" or "style" what OptiPath considers a "feature"). The seriation technique can be set in the Seriations table.
The underlying assumption in archaeological occurrence seriation is that a feature will normally be introduced only once in the evolution of an artifact type - once the feature has appeared and then been absent in artifacts for a period of time it will not reappear. Most implementations of occurrence seriation attempt to order the artifacts temporally so as to minimize the number of times that a distinct feature is introduced into the archaeological record. Equivalently, occurrence seriation tries to minimize the total number of transitions (from absent to present, and present to absent) for all features. If a perfect seriation exists, the total number of transitions will be two times the number of features (where each feature is assumed to be absent at some point both earlier and later than the artifacts in the sample being analyzed).
Occurrence seriation is a special case of the Optimal Path seriation model. Setting the seriation parameter Technique to Occurrence specifies OptiPath's standard implementation of occurrence seriation. In this case OptiPath uses the Optimal Path seriation model with Hamming distance. Data may take on any values but zeroes and blanks are both assumed to represent an absence of the feature (class or style) in question. All other values are taken to indicate the presence of the feature. Setting the seriation parameter Technique to Occurrence causes OptiPath to automatically set the feature parameters Data, Ranks, Metric, Normalize, Transition, Earlier, Later, Blanks and Zeroes to specific values.
The following are the default feature parameter settings for occurrence seriation. To change them you must first select the Custom Seriation technique. With Custom seriation OptiPath allows you to simultaneously treat some features as occurrences/absences and others as classifications or as ranked or measured data - see Data in the Features table.
Data = Classed Ranks = 1 Metric = Hamming Normalize = No Transition = 0.5 Earlier = Absent Later = Absent Blanks = Absent Zeroes = Absent
These settings result in any non-zero entry in the Data being interpreted as indicating the presence of a feature (class or style) and any blank or zero in the data being interpreted as the absence. If you want zeroes to be interpreted as values and indicating the presence of the feature, you should set the seriation parameter Technique to Custom and the feature parameter Zeroes to Value (and the rest of the parameters as above). If you want blanks to be interpreted as unknown, you should set the seriation parameter Technique to Custom and the feature parameter Blanks to Unknown (and the rest of the parameters as above).
With the settings above, all non-zero entries will be converted to "1". All blanks and zeroes will be converted to "Absent". For example, if your data consists entirely of zeroes and ones, the zeroes will be interpreted as absences (with a value of "Absent") and the ones as presences (with a value of "1"). As another example, the data for a feature might contain the values "3", "7", "notched", "palmate", "serrated" and "lobed", as well as blanks. In this case the blanks would be converted to "Absent" and all other entries to "1". If the data also contained an entry "0" it would be converted to "Absent". To see the effect of your settings, look at processed data in the Values table.
Warning! If your data are not numbers but alphanumeric values still representing absence and presence such as ("absent" and "present" or "no" and "yes" or "zero" and "one"), the results will not be the same. OptiPath will interpret "absent" as present (giving it the value "1"). The advantage of using zero/one data over "absent"/"present" is that OptiPath can recognize zeroes and treat them as absences (via the Zeroes parameter) but OptiPath has no facility to recognize words like "absent" or "no" or "zero" and treat them specially. When using the words "absent" and "present", OptiPath will not identify absences as such and will not apply the Transition penalty in a transition from "absent" to "present" but will apply the penalty in a transition from "absent" to a blank (with Blanks = Absent). If you use "no" and "yes", both will be assigned a value of "1" and OptiPath will be indifferent between seriations resulting in no-yes-no (two absence-presence transitions, namely the transitions from earlier and to later) or yes-no-yes (also two absence-presence transitions) whereas if you were instead using the numbers 0 and 1 (which would be assigned values of "Absent" and "1" respectively), OptiPath would prefer 0-1-0 (two absence-presence transitions) to 1-0-1 (four absence-presence transitions, including the transitions from earlier and to later). The results are different.
In occurrence seriation, careful thought should be put into setting the feature parameters appropriately - see Setting the Earlier, Later, Blanks, Zeroes and Transition Parameters.