Return data for the subtaxa of each taxon in an taxonomy()
or taxmap()
object.
obj$subtaxa(subset = NULL, recursive = TRUE, simplify = FALSE, include_input = FALSE, value = "taxon_indexes") subtaxa(obj, subset = NULL, recursive = TRUE, simplify = FALSE, include_input = FALSE, value = "taxon_indexes")
obj | The |
---|---|
subset | Taxon IDs, TRUE/FALSE vector, or taxon indexes to find subtaxa for.
Default: All taxa in |
recursive | ( |
simplify | ( |
include_input | ( |
value | What data to return. This is usually the name of column in a
table in |
If simplify = FALSE
, then a list of vectors are returned
corresponding to the target
argument. If simplify = TRUE
,
then the unique values are returned in a single vector.
Other taxonomy indexing functions:
branches()
,
internodes()
,
leaves()
,
roots()
,
stems()
,
supertaxa()
# return the indexes for subtaxa for each taxon subtaxa(ex_taxmap)#> $b #> d h m i n e j o f k p #> 3 7 12 8 13 4 9 14 5 10 15 #> #> $c #> g l q r #> 6 11 16 17 #> #> $d #> h m i n #> 7 12 8 13 #> #> $e #> j o #> 9 14 #> #> $f #> k p #> 10 15 #> #> $g #> l q r #> 11 16 17 #> #> $h #> m #> 12 #> #> $i #> n #> 13 #> #> $j #> o #> 14 #> #> $k #> p #> 15 #> #> $l #> q r #> 16 17 #> #> $m #> named integer(0) #> #> $n #> named integer(0) #> #> $o #> named integer(0) #> #> $p #> named integer(0) #> #> $q #> named integer(0) #> #> $r #> named integer(0) #># Only return data for some taxa using taxon indexes subtaxa(ex_taxmap, subset = 1:3)#> $b #> d h m i n e j o f k p #> 3 7 12 8 13 4 9 14 5 10 15 #> #> $c #> g l q r #> 6 11 16 17 #> #> $d #> h m i n #> 7 12 8 13 #>#> $d #> h m i n #> 7 12 8 13 #> #> $e #> j o #> 9 14 #># Only return data for some taxa using logical tests subtaxa(ex_taxmap, subset = taxon_ranks == "genus")#> $h #> m #> 12 #> #> $i #> n #> 13 #> #> $j #> o #> 14 #> #> $k #> p #> 15 #> #> $l #> q r #> 16 17 #># Only return subtaxa one level below subtaxa(ex_taxmap, recursive = FALSE)#> $b #> d e f #> 3 4 5 #> #> $c #> g #> 6 #> #> $d #> h i #> 7 8 #> #> $e #> j #> 9 #> #> $f #> k #> 10 #> #> $g #> l #> 11 #> #> $h #> m #> 12 #> #> $i #> n #> 13 #> #> $j #> o #> 14 #> #> $k #> p #> 15 #> #> $l #> q r #> 16 17 #> #> $m #> named integer(0) #> #> $n #> named integer(0) #> #> $o #> named integer(0) #> #> $p #> named integer(0) #> #> $q #> named integer(0) #> #> $r #> named integer(0) #># Only return subtaxa some number of ranks below subtaxa(ex_taxmap, recursive = 2)#> $b #> d h i e j f k #> 3 7 8 4 9 5 10 #> #> $c #> g l #> 6 11 #> #> $d #> h m i n #> 7 12 8 13 #> #> $e #> j o #> 9 14 #> #> $f #> k p #> 10 15 #> #> $g #> l q r #> 11 16 17 #> #> $h #> m #> 12 #> #> $i #> n #> 13 #> #> $j #> o #> 14 #> #> $k #> p #> 15 #> #> $l #> q r #> 16 17 #> #> $m #> named integer(0) #> #> $n #> named integer(0) #> #> $o #> named integer(0) #> #> $p #> named integer(0) #> #> $q #> named integer(0) #> #> $r #> named integer(0) #># Return something besides taxon indexes subtaxa(ex_taxmap, value = "taxon_names")#> $b #> d h m i n #> "Felidae" "Panthera" "tigris" "Felis" "catus" #> e j o f k #> "Notoryctidae" "Notoryctes" "typhlops" "Hominidae" "homo" #> p #> "sapiens" #> #> $c #> g l q r #> "Solanaceae" "Solanum" "lycopersicum" "tuberosum" #> #> $d #> h m i n #> "Panthera" "tigris" "Felis" "catus" #> #> $e #> j o #> "Notoryctes" "typhlops" #> #> $f #> k p #> "homo" "sapiens" #> #> $g #> l q r #> "Solanum" "lycopersicum" "tuberosum" #> #> $h #> m #> "tigris" #> #> $i #> n #> "catus" #> #> $j #> o #> "typhlops" #> #> $k #> p #> "sapiens" #> #> $l #> q r #> "lycopersicum" "tuberosum" #> #> $m #> named character(0) #> #> $n #> named character(0) #> #> $o #> named character(0) #> #> $p #> named character(0) #> #> $q #> named character(0) #> #> $r #> named character(0) #>