Extract all clades present in the lineages

Usage

get_all_clades(lineage, simplify = TRUE)

Arguments

lineage: string. Vector of lineages.
simplify: logical. Should the output be a vector or a dataframe?

Value

The clades present in the lineage. Vector of ordered strings or data.frame.

Details

If a clade correspond to different ranks (e.g. Actinobacteria is both a phylum and a clade), it will be displayed only one time when simplify is set to TRUE. It is also the case for different clades with same name and same rank when simplify is set to FALSE.

Examples

lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
lineage3 <- "k__Bacteria|p__Actinobacteria|c__Actinobacteria"
get_all_clades(c(lineage1, lineage2, lineage3))
#> [1] "Actinobacteria"   "Bacteria"         "Clostridia"       "Firmicutes"      
#> [5] "Verrucomicrobia"  "Verrucomicrobiae"
get_all_clades(c(lineage1, lineage2, lineage3), simplify = FALSE)
#>              clade    rank
#> 6   Actinobacteria  phylum
#> 7   Actinobacteria   class
#> 1         Bacteria kingdom
#> 5       Clostridia   class
#> 4       Firmicutes  phylum
#> 2  Verrucomicrobia  phylum
#> 3 Verrucomicrobiae   class