Extract a subset of the taxonomy for a set of ids

Extract a subset of the taxonomy for a set of ids

extract_taxo(db, taxon_ids, recursive = TRUE)

Arguments

db	a connection to an EcoTaxa database (from db_connect_ecotaxa()).
taxon_ids	internal, numeric ids of the taxa.
recursive	when TRUE, extract the full taxonomy, until the root.

See also

Other taxonomy-related functions: ancestors(), as.taxo(), children(), descendants(), is_leaf(), lineage(), parent(), taxo_id(), taxo_name()

Examples

db <- db_connect_ecotaxa()
extract_taxo(db, 84000:84003)
#>       id                  name parent_id
#> 1  84000       Carcinus maenas     83439
#> 2  84001 Caridina multidentata     83647
#> 3  84002     Caridina formosae     83647
#> 4  84003   Carpilius maculatus     83438
#> 5  83439              Carcinus     81916
#> 6  83647              Caridina     81911
#> 7  83438             Carpilius     81916
#> 8  81916             Brachyura     78372
#> 9  81911               Caridea     78372
#> 10 78372           Pleocyemata     45043
#> 11 45043              Decapoda     25824
#> 12 25824        Eumalacostraca     16622
#> 13 16622          Malacostraca     12846
#> 14 12846             Crustacea     11517
#> 15 11517            Arthropoda      2367
#> 16  2367               Metazoa       382
#> 17   382               Holozoa         8
#> 18     8          Opisthokonta         2
#> 19     2             Eukaryota         1
#> 20     1                living        NA
extract_taxo(db, 84000:84003, recursive=FALSE)
#>      id parent_id                  name id_source creation_datetime
#> 1 84000     83439       Carcinus maenas     46613              <NA>
#> 2 84001     83647 Caridina multidentata     46616              <NA>
#> 3 84002     83647     Caridina formosae     46615              <NA>
#> 4 84003     83438   Carpilius maculatus     46621              <NA>
#>   creator_email          display_name id_instance lastupdate_datetime rename_to
#> 1          <NA>       Carcinus maenas          NA          2018-01-02        NA
#> 2          <NA> Caridina multidentata          NA          2018-01-02        NA
#> 3          <NA>     Caridina formosae          NA          2018-01-02        NA
#> 4          <NA>   Carpilius maculatus          NA          2018-01-02        NA
#>   source_desc source_url taxostatus taxotype
#> 1        <NA>       <NA>          A        P
#> 2        <NA>       <NA>          A        P
#> 3        <NA>       <NA>          A        P
#> 4        <NA>       <NA>          A        P