Test if a lineage belongs to a clade — is_clade • yatah

Test if a lineage belongs to a clade

Usage

is_clade(lineage, clade, rank = c(".", yatah::all_ranks))

Arguments

lineage: string. Vector of lineages.
clade: string.
rank: string. One of c("kingdom", "phylum", "class", "order", "family", "genus", "species", "strain") with partial matching.

Value

logical.

Details

If rank is set to ., clade is looked for among all ranks.

Examples

lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
is_clade(c(lineage1, lineage2), clade = "Verrucomicrobia", rank = "phylum")
#> [1]  TRUE FALSE
is_clade(c(lineage1, lineage2), clade = "Clostridia")
#> [1] FALSE  TRUE