taxize 0.0.3

Get taxonomic hierarchy for a given taxon ID.

Usage

classification(x, ID = NULL, ...)

classification(x, ...)

classification(x, ...)

Arguments

x
IDs from get_tsn() or get_uid().
ID
type of identifier, either 'uid' or 'tsn'
...
Currently not used

Value

Classification of taxons in a list of data.frames.

Description

Get taxonomic hierarchy for a given taxon ID.

Note

If IDs are supplied directly (not from the get_* functions) use the methods classification.ncbi() or classification.tsn() directly. See examples.

Examples

classification(get_uid(c("Chironomus riparius", "aaa vva")))



Retrieving data for species ' Chironomus riparius '

Retrieving data for species ' aaa vva '



[[1]]
              ScientificName         Rank     UID
1         cellular organisms      no rank  131567
2                  Eukaryota superkingdom    2759
3               Opisthokonta      no rank   33154
4                    Metazoa      kingdom   33208
5                  Eumetazoa      no rank    6072
6                  Bilateria      no rank   33213
7                Protostomia      no rank   33317
8                  Ecdysozoa      no rank 1206794
9              Panarthropoda      no rank   88770
10                Arthropoda       phylum    6656
11               Mandibulata      no rank  197563
12              Pancrustacea      no rank  197562
13                  Hexapoda   superclass    6960
14                   Insecta        class   50557
15                Dicondylia      no rank   85512
16                 Pterygota      no rank    7496
17                  Neoptera     subclass   33340
18             Endopterygota   infraclass   33392
19                   Diptera        order    7147
20                Nematocera     suborder    7148
21              Culicimorpha   infraorder   43786
22             Chironomoidea  superfamily   41828
23              Chironomidae       family    7149
24              Chironominae    subfamily   54970
25               Chironomini        tribe   72530
26                Chironomus        genus    7150
27 Chironomus incertae sedis      no rank 1165752
28       Chironomus riparius      species  315576

[[2]]
[1] NA




classification(get_tsn(c("Chironomus riparius", "aaa vva"), "sciname"))



Retrieving data for species ' Chironomus riparius '

Retrieving data for species ' aaa vva '


http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=129313
Error in out$tsn: $ operator is invalid for atomic vectors


# must specify Identifier, when not used with get_*()
classification(315576, ID = "uid")


[[1]]
              ScientificName         Rank     UID
1         cellular organisms      no rank  131567
2                  Eukaryota superkingdom    2759
3               Opisthokonta      no rank   33154
4                    Metazoa      kingdom   33208
5                  Eumetazoa      no rank    6072
6                  Bilateria      no rank   33213
7                Protostomia      no rank   33317
8                  Ecdysozoa      no rank 1206794
9              Panarthropoda      no rank   88770
10                Arthropoda       phylum    6656
11               Mandibulata      no rank  197563
12              Pancrustacea      no rank  197562
13                  Hexapoda   superclass    6960
14                   Insecta        class   50557
15                Dicondylia      no rank   85512
16                 Pterygota      no rank    7496
17                  Neoptera     subclass   33340
18             Endopterygota   infraclass   33392
19                   Diptera        order    7147
20                Nematocera     suborder    7148
21              Culicimorpha   infraorder   43786
22             Chironomoidea  superfamily   41828
23              Chironomidae       family    7149
24              Chironominae    subfamily   54970
25               Chironomini        tribe   72530
26                Chironomus        genus    7150
27 Chironomus incertae sedis      no rank 1165752
28       Chironomus riparius      species  315576




classification(180544, "tsn")

http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=180544

[[1]]
   parentName parentTsn   rankName        taxonName    tsn
1                          Kingdom         Animalia 202423
2    Animalia    202423     Phylum         Chordata 158852
3    Chordata    158852  Subphylum       Vertebrata 331030
4  Vertebrata    331030      Class         Mammalia 179913
5    Mammalia    179913   Subclass           Theria 179916
6      Theria    179916 Infraclass         Eutheria 179925
7    Eutheria    179925      Order        Carnivora 180539
8   Carnivora    180539   Suborder       Caniformia 552303
9  Caniformia    552303     Family          Ursidae 180540
10    Ursidae    180540      Genus            Ursus 180541
11      Ursus    180541    Species Ursus americanus 180544