Exact Principal Balances

coda.base can calculate the PB with the function pb_basis(). Function pb_basis() needs the parameter method to be set. To obtain the PB users needs to set method = "exact".

B1 = pb_basis(X, method = "exact")

Where the obtained sequential binary partition can be summarized with the following sequential binary tree:

plot_balance(B1)

apply(coordinates(X, B1), 2, var)
#>      pb1      pb2      pb3      pb4      pb5      pb6      pb7 
#> 0.663216 0.085733 0.046135 0.044113 0.032890 0.028590 0.008179

When method is set to "exact", exhaustive search is performed to obtain the PB. The time needed to calculate the PB grows exponentially regarding the number of parts of X. To iterate through all the possibilities, CoDaPack uses the algorithm Ruskey (1993). Currently, exhaustive search can find the PB of a compositional data set with 20 parts in a reasonable amount of time (5 minutes approximately).

When the number of part is higher, the exact method should be discarded in favor of other alternatives. Different alternatives are available in Pawlowsky-Glahn, Egozcue, and Tolosan-Delgado (2011) and Martín-Fernández et al. (2017). Between these alternatives, the once that can be implemented are agglomerate partition approach based on the Ward method Martín-Fernández et al. (2017) and the approximation based on a reduced approximation to the principal components (Martín-Fernández et al. 2017).

Ward Method for Parts

For a composition \(X\), Pawlowsky-Glahn, Egozcue, and Tolosan-Delgado (2011) proposed to build the variation array and use it to produce a matrix distance. The variation array calculates the variance between a pair of logratios.

D = as.dist(variation_array(X))
D
#>            cs   jxcat     erc     psc   catsp     cup      pp
#> jxcat 0.62079                                                
#> erc   0.39636 0.08823                                        
#> psc   0.04887 0.53876 0.29338                                
#> catsp 0.06682 0.54951 0.29768 0.01636                        
#> cup   0.48118 0.07179 0.05809 0.36163 0.35432                
#> pp    0.12424 0.40944 0.20351 0.10318 0.14361 0.32193        
#> other 0.07018 0.56344 0.36363 0.07197 0.07462 0.37428 0.20308

Combining pairs with lower variance, it is expected to get a final merging with high variability.

B2 = pb_basis(X, method = 'cluster')
plot_balance(B2)

apply(coordinates(X, B2), 2, var)
#>      pb1      pb2      pb3      pb4      pb5      pb6      pb7 
#> 0.651569 0.097381 0.043659 0.043188 0.035838 0.029044 0.008179

Constrained PCs Algorithm

B3 = pb_basis(X, method = 'constrained')
plot_balance(B3)

apply(coordinates(X, B3), 2, var)
#>      pb1      pb2      pb3      pb4      pb5      pb6      pb7 
#> 0.663216 0.085733 0.046135 0.044113 0.032890 0.028590 0.008179