Artifacts
Artifacts are the items being seriated. OptiPath has been developed as a tool in archaeology although it can be used in other fields as well. In deference to archaeologists, we use the term 'artifact' rather than 'object' or 'item'. Archaeologists often deal with collections, or assemblages), of artifacts rather than individual artifacts. OptiPath can work with collections as individual artifacts, or it can build assemblages from individual artifact data.
The object of seriation is to determine an ordering, or seriation, of a number of objects, or artifacts, that replicates as closely as possible their historical order of creation. To do this, OptiPath relies on the assumption that the artifacts share characteristics or features whose measure evolves gradually over time. The ordering of artifacts that produces the most gradual (or unimodal if the user chooses) evolution of all features for all artifacts is considered the optimal seriation.
By choosing Assemblages in the seriation parameters or by selecting
Use Assemblages from the Assemblage menu or by clicking the Assemblages button
on the toolbar, you can direct OptiPath to classify
individual artifacts by their assemblage and then seriate the assemblages rather
than the artifacts themselves (see Assemblages).
The Assemblages button is a toggle, being replaced by the Artifacts button
when using
assemblages.
Artifacts Menu
Select/Edit allows you to open the artifacts table and create, delete, select and edit the artifacts and edit their parameters.
Show/Hide Data is a toggle that specifies whether artifact feature data are to be displayed in the artifacts table. This item toggles between Show Data and Hide Data. This menu item is disabled if the artifacts table is not open.
Show/Hide Results is a toggle that specifies whether seriation results are to be displayed in the artifacts table. This item toggles between Show Results and Hide Results. This menu item is disabled if the artifacts table is not open.
Include All allows you to include all currently excluded artifacts in the seriation.
Sort -> Index allows you to reindex all included artifacts in the order they currently appear in the Artifacts table. This is useful for saving a particular seriation (sort the table by the Order column by clicking on the column header and then click Sort -> Index in the Artifacts menu). The Order Errors term in the Seriations table will then give an indication of how different a subsequent seriation is.
Sort -> Order allows you to reorder all included artifacts in the order they currently appear in the Artifacts table. This is useful for creating a seriation (sort the table by any column by clicking on the column header and then click Sort -> Order in the Artifacts menu). The Results will be updated to reflect the new seriation.
Artifacts Table
In the Artifacts table you may add, delete, exclude and edit artifacts and their data. The rows of the Artifacts table may be sorted by the values of any column by clicking on the header for that column. Clicking a second time will reverse the order.
Right clicking on the table will bring up a pop up menu of available actions.
There are two rows with artifacts labeled EARLIER and LATER that are in green. These are virtual artifacts added by OptiPath to represent artifacts earlier and later than those in your data. The entries in these rows are read only and cannot be edited. However, the entries can be modified by editing the corresponding entries in the Seriations table.
If Show Results has been selected in the Artifacts menu, there will be a row in red that shows the unimodal index for the seriation and for each feature.
By choosing Hide Results and Hide Data in the Artifacts menu, you can reduce the number of fields displayed.
You can enter and edit your data in this table or you can edit them in the Data table. There are a number of parameters associated with each artifact:
Exclude allows you to exclude an artifact temporarily from your seriation. The alternative is to delete the artifact in which case all information and data related to the artifact will be lost to this seriation permanently. In contrast, using Exclude allows you to resurrect the artifact and its data by clearing the Exclude field. All Exclude fields can be cleared simultaneously by selecting Include All from the Artifacts menu. Excluded items are greyed out and cannot be edited.
Index is an integer value assigned to an artifact that allows you to sort artifacts in tables.
Artifact is a name that uniquely identifies the artifact. Artifact names are restricted to 50 characters. The artifact name is required for each artifact. An artifact cannot have the same name as another artifact and cannot have the same name as an assemblage. The following names are reserved for use by OptiPath and cannot be used as artifact names: Earlier, Later, Unimodal Index.
Assemblage allows the user to assign each
artifact to an assemblage. This allows you to enter
data for individual artifacts but have OptiPath seriate sets, or assemblages,
of artifacts. Assemblages can only be assigned by selecting an assemblage from a list.
To do this, you must first create assemblages. The
assemblages you create will be available for assignment to artifacts. To
have OptiPath seriate assemblages rather than artifacts, you must
set the Assemblages parameter for the seriation.
The easiest way to do this is to select Use Assemblages from
the Assemblages menu or by clicking the Assemblages button
on the toolbar.
Description is an optional description that can be entered for each artifact. There is no limit to the length of a description.
Earliest is a value representing the earliest possible date that can be assigned to this artifact. The Earliest date should not be less than the overall Earliest date for the seriation which is set in the Seriations table. Assigning Earliest dates other than Earliest date for the overall seriation will generally result in longer computation times when seriating.
Latest is a value representing the latest possible date that can be assigned to the artifact. The Latest date should not be greater than the overall Latest date for the seriation which is set in the Seriations table. Assigning Latest dates other than Latest date for the overall seriation will generally result in longer computation times when seriating.
Use Dates allows you to use or ignore the Earliest and Latest dates for this artifact in seriating when Use Dates is checked on the Seriations table. Use Dates on the seriation tells the algorithm whether to use Earliest and Latest dates, and Use Dates on the artifacts tells algorithms which dates to use, artifact by artifact. When Use Dates is not checked on the Seriations table, Use Dates tells OptiPath which dates to use when computing date Errors. If you right click on the Use Dates column a pop up window will appear allowing you to select or unselect Use Dates for all of the artifacts simultaneously.
Order indicates an artifact's sequential (ordinal) position in a
seriation. This field can be modified by the user. You can also reverse
the order of the seriation by choosing Reverse from the Seriate menu or the
Results menu or by clicking the Reverse button
on the
toolbar.
Date indicates an artifact's date as estimated by OptiPath in performing a seriation. This field cannot be modified by the user. This information can also be seen in the Results table.
Distance gives an artifact's distance along the path computed by OptiPath in performing a seriation expressed as a fraction of the total distance of the path (the total path length is normalized to 1). This field cannot be modified by the user. This information can also be seen in the Results table.
Rate indicates an artifact's rate of change from the previous artifact in the seration as computed by OptiPath. The rate of change is the difference in distances divided by the difference in dates. This field cannot be modified by the user. This information can also be seen in the Results table.
Features - there is a separate column for each not excluded feature. Feature names cannot be edited in this table. Each cell in a feature column reflects the value of the measure for that feature for artifact in the corresponding row. Values can be numbers or letters or words, depending upon the feature data type.
Warning! The following entries in feature data will be interpreted literally:
Present & Zero
Absent & Zero
Present & Unknown
Absent & Unknown
Unknown & Zero
Unknown
These six values (they are case sensitive) are the only allowed values for Earlier and Later, and Blanks and Zeroes. However, OptiPath will interpret them literally wherever they appear in the feature data. This means with an entry of Present & Zero the feature would be considered as having a value 0 and the item (artifact or assemblage) would incur a transition penalty if preceded or succeeded by an item for which the feature is absent.