3.1 Ordination procedure

prot1 <- apply_ordination(cleanAmphorae[!isShipwreck,], # no shipwrecks
                          "1", # select protocol 1
                          coda_override = chemVars16,
                          coda_transformation_method = "ILR")
#> sROC 0.1-2 loaded
#> [1] "78.24% of variance explained in 2D"
#> [1] "86.54% of variance explained in 3D"
#> [1] "Protocol 1 ended."

The outcome is an ordination object. In this case, it is the output of pcaCoDa function in robCompositions package, in addition to several extra information, such as the transformed data (‘transformed_data’), the distance matrix (‘dist_matrix’), and the ready-to-plot texts indicating the fitness of the 2D/3D projections respect the distance matrix (‘sub2d’, ‘sub3d’). The later are printed in the console once the object is created.

class(prot1)
#> [1] "pcaCoDa"

names(prot1)
#>  [1] "scores"                "loadings"             
#>  [3] "eigenvalues"           "method"               
#>  [5] "princompOutputClr"     "mult_comp"            
#>  [7] "seed"                  "init_seed"            
#>  [9] "samples"               "sub2D"                
#> [11] "sub3D"                 "transformation_method"
#> [13] "transformed_data"      "dist_matrix"          
#> [15] "name"