I'm following this tutorial to compare the 16S taxonomies (created using RDP classifier command line version) of two different samples.

But I'm stuck at "If you open the text file /proj/g2013206/metagenomics/r_commands.txt you can copy and paste all of this code into R (or use the source command) and this will give you the matrices and vectors below". The "r_commands.txt" file isn't available anywhere and I'm an R noob so I don't know how to generate the different rank matrices from my data. If anyone could provide me with this file or teach me how to generate these rank matrices that would be amazing, thank you! My input counts data looks like this:

Taxon   Sample1     Sample2
Root    29159   29159
Root;Archaea    123     123
Root;Archaea;"Crenarchaeota";Thermoprotei       44      44
Root;Archaea;"Crenarchaeota";Thermoprotei;Acidilobales;Acidilobaceae;Acidilobus 1       1
Root;Archaea;"Crenarchaeota";Thermoprotei;Sulfolobales;Sulfolobaceae;Metallosphaera     1       1
Root;Archaea;"Euryarchaeota"    158     158
Root;Archaea;"Euryarchaeota";"Methanomicrobia"  8       8
Root;Archaea;"Euryarchaeota";"Methanomicrobia";Methanomicrobiales       801     801
Root;Archaea;"Euryarchaeota";"Methanomicrobia";Methanomicrobiales;Methanomicrobiaceae   134     134