6.1 Ordination procedure

As protocol 3, protocol 4 performs PCoA on a distance matrix calculated with Extended Gower coefficient of dissimilarity, combining Euclidean distances on transformed compositional data (50%) and RRD on ranked petrographic data (50%).

prot4_2d <- apply_ordination(cleanAmphorae[!isShipwreck,],
                             "4", # select protocol 4
                             exception_columns = excep_cols,
                             variable_tags = varCode,
                             coda_override = chemVars16,
                             coda_transformation_method = "CLR")

prot4_3d <- apply_ordination(cleanAmphorae[!isShipwreck,],
                             "4", # select protocol 4
                             exception_columns = excep_cols,
                             variable_tags = varCode,
                             coda_override = chemVars16,
                             coda_transformation_method = "CLR",
                             dimensions = 3)

However, protocol 4 uses a finer selection of petrographic variables, which are considered indicative of provenance (raw materials) rather than technology. Compare the number of variables in protocol 3 and 4:

Protocol 3	Protocol 4
78	59