5.1 Ordination procedure

Protocol 3 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%). As in protocol 2, PCoA requires specifying the number of dimensions and so you must 2D and 3D ordination objects separately:

prot3_2d <- apply_ordination(cleanAmphorae[!isShipwreck,], # no shipwrecks
                             "3", # select protocol 3
                             exception_columns = excep_cols,
                             variable_tags = varCode,
                             coda_override = chemVars16,
                             coda_transformation_method = "CLR")

prot3_3d <- apply_ordination(cleanAmphorae[!isShipwreck,], # no shipwrecks
                             "3", # select protocol 3
                             exception_columns = excep_cols,
                             variable_tags = varCode,
                             coda_override = chemVars16,
                             coda_transformation = "CLR",
                             dimensions = 3)