There are two ways to call this function:
Details
If the rank you are interested in is in the standard list, just supply it as an argument.
If not, delete all taxon variables except taxon_id and the ranks you are still interested in prior to calling this function.
Examples
urt %>% aggregate_taxa(rank = "class")
#> $samples
#> # A tibble: 217 × 9
#> run condition participant location method plate passes_qc sample sample_id
#> <chr> <chr> <chr> <chr> <chr> <dbl> <lgl> <chr> <chr>
#> 1 20161… CON CON100 NF S 3 TRUE CON10… s1
#> 2 20161… CON CON100 N S 3 TRUE CON10… s2
#> 3 20161… CON CON10 NF A 1 TRUE CON10… s3
#> 4 20161… CON CON10 NF S 1 TRUE CON10… s4
#> 5 20161… CON CON11 NF S 1 TRUE CON11… s5
#> 6 20161… CON CON11 N S 1 TRUE CON11… s6
#> 7 20161… CON CON12 NF S 1 TRUE CON12… s7
#> 8 20161… CON CON13 NF S 1 TRUE CON13… s8
#> 9 20161… CON CON13 N S 1 TRUE CON13… s9
#> 10 20161… CON CON14 NF S 1 TRUE CON14… s10
#> # ℹ 207 more rows
#>
#> $taxa
#> # A tibble: 65 × 6
#> kingdom phylum class taxon_id taxon_name taxon
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Bacteria Firmicutes Bacilli t2 Bacilli Baci…
#> 2 Bacteria Actinobacteria Actinobacteria t5 Actinobacteria Acti…
#> 3 Bacteria Proteobacteria Gammaproteobacteria t1 Gammaproteobact… Gamm…
#> 4 Bacteria Firmicutes Clostridia t6 Clostridia Clos…
#> 5 Bacteria Proteobacteria Betaproteobacteria t3 Betaproteobacte… Beta…
#> 6 Bacteria Fusobacteria Fusobacteriia t4 Fusobacteriia Fuso…
#> 7 Bacteria Firmicutes Negativicutes t7 Negativicutes Nega…
#> 8 Bacteria Bacteroidetes Bacteroidia t8 Bacteroidia Bact…
#> 9 Bacteria Proteobacteria Alphaproteobacteria t9 Alphaproteobact… Alph…
#> 10 Bacteria Proteobacteria Epsilonproteobacteria t11 Epsilonproteoba… Epsi…
#> # ℹ 55 more rows
#>
#> $counts
#> # A tibble: 2,064 × 3
#> taxon_id sample_id count
#> <chr> <chr> <dbl>
#> 1 t1 s1 85
#> 2 t1 s10 15606
#> 3 t1 s100 1103
#> 4 t1 s102 2777
#> 5 t1 s103 282
#> 6 t1 s104 587
#> 7 t1 s105 376
#> 8 t1 s106 118
#> 9 t1 s107 1561
#> 10 t1 s108 1628
#> # ℹ 2,054 more rows
#>
#> $rank_names
#> [1] "kingdom" "phylum" "class"
#>
#> attr(,"class")
#> [1] "tidytacos"