taxize 0.0.3

Retrieve all taxonomic hierarchy from given EOL taxonID.

Usage

eol_hierarchy(taxonid, common_names = NULL, synonyms = NULL, usekey = FALSE, returntype = "data.frame",
  url = "http://www.eol.org/api/hierarchy_entries/1.0/", key = NULL)

Arguments

taxonid
the EOL page identifier (character)
common_names
Return common names or not (defaults to returning them, given commonnames=0 if not)
synonyms
Return synonyms or not (defaults to returning them, given synonyms=0 if not)
usekey
use your API key or not (TRUE or FALSE)
returntype
one of "list" of "data.frame" (character)
url
The EOL url for the function (should be left to default).
key
Your EOL API key; loads from .Rprofile.

Value

List or dataframe of XXXX.

Description

Retrieve all taxonomic hierarchy from given EOL taxonID.

Details

It's possible to return JSON or XML with the EOL API. However, this function only returns JSON for now.

Examples

pageid <- eol_search('Pomatomus')$id[1]

http://eol.org/api/search/Pomatomus.json?key=52987dc6505de77c6c9345e8e8068f74ffb52de6

out <- eol_pages(taxonconceptID=pageid)

http://eol.org/api/pages/1.0/24805.json

eol_hierarchy(out[out$nameAccordingTo == "NCBI Taxonomy", "identifier"])

http://www.eol.org/api/hierarchy_entries/1.0/39153619.json?common_names=1&synonyms=1

   sourceIdentifier  taxonID parentNameUsageID taxonConceptID     scientificName
1            131567 38500412                 0       11660866 Cellular organisms
2              2759 38714833          38500412        2908256          Eukaryota
3             33154 38842262          38714833        2910700       Opisthokonta
4             33208 38913758          38842262              1            Metazoa
5              6072 38915309          38913758       10380067          Eumetazoa
6             33213 38920151          38915309        3014411          Bilateria
7             33316 38931382          38920151       11995650          Coelomata
8             33511 39145054          38931382        8814528      Deuterostomia
9              7711 39147281          39145054            694           Chordata
10            89593 39147686          39147281        5004126           Craniata
11             7742 39147687          39147686        2774383         Vertebrata
12             7776 39147688          39147687       12094272      Gnathostomata
13           117570 39148878          39147688        4656087         Teleostomi
14           117571 39148879          39148878       10459961       Euteleostomi
15             7898 39148880          39148879           1905     Actinopterygii
16           186623 39148908          39148880       12095116        Actinopteri
17            41665 39148987          39148908        2775792        Neopterygii
18            32443 39149008          39148987        2775808          Teleostei
19           186624 39149256          39149008       12095400       Elopocephala
20           186625 39149790          39149256       12095755      Clupeocephala
21            32447 39149791          39149790       12095756        Euteleostei
22           186839 39150305          39149791       12096153          Neognathi
23           123365 39150333          39150305       12096174       Neoteleostei
24           123366 39150601          39150333       12096269       Eurypterygii
25           123367 39150813          39150601       12096393      Ctenosquamata
26           123368 39151028          39150813        4657596      Acanthomorpha
27           123369 39151075          39151028       12096554    Euacanthomorpha
28           123370 39151089          39151075       12096563 Holacanthopterygii
29            32455 39151090          39151089           8228    Acanthopterygii
30           129947 39151232          39151090       12096677  Euacanthopterygii
31            32485 39151366          39151232        4656110        Percomorpha
32             8111 39152344          39151366           5184        Perciformes
33             8112 39152345          39152344        2793360          Percoidei
34            30864 39153618          39152345           5258        Pomatomidae
                                                              source    taxonRank
1  http://eol.org/pages/11660866/hierarchy_entries/38500412/overview         
2   http://eol.org/pages/2908256/hierarchy_entries/38714833/overview superkingdom
3   http://eol.org/pages/2910700/hierarchy_entries/38842262/overview         
4         http://eol.org/pages/1/hierarchy_entries/38913758/overview      kingdom
5  http://eol.org/pages/10380067/hierarchy_entries/38915309/overview         
6   http://eol.org/pages/3014411/hierarchy_entries/38920151/overview         
7  http://eol.org/pages/11995650/hierarchy_entries/38931382/overview         
8   http://eol.org/pages/8814528/hierarchy_entries/39145054/overview         
9       http://eol.org/pages/694/hierarchy_entries/39147281/overview       phylum
10  http://eol.org/pages/5004126/hierarchy_entries/39147686/overview    subphylum
11  http://eol.org/pages/2774383/hierarchy_entries/39147687/overview         
12 http://eol.org/pages/12094272/hierarchy_entries/39147688/overview   superclass
13  http://eol.org/pages/4656087/hierarchy_entries/39148878/overview         
14 http://eol.org/pages/10459961/hierarchy_entries/39148879/overview         
15     http://eol.org/pages/1905/hierarchy_entries/39148880/overview        class
16 http://eol.org/pages/12095116/hierarchy_entries/39148908/overview         
17  http://eol.org/pages/2775792/hierarchy_entries/39148987/overview         
18  http://eol.org/pages/2775808/hierarchy_entries/39149008/overview         
19 http://eol.org/pages/12095400/hierarchy_entries/39149256/overview         
20 http://eol.org/pages/12095755/hierarchy_entries/39149790/overview         
21 http://eol.org/pages/12095756/hierarchy_entries/39149791/overview         
22 http://eol.org/pages/12096153/hierarchy_entries/39150305/overview         
23 http://eol.org/pages/12096174/hierarchy_entries/39150333/overview         
24 http://eol.org/pages/12096269/hierarchy_entries/39150601/overview         
25 http://eol.org/pages/12096393/hierarchy_entries/39150813/overview         
26  http://eol.org/pages/4657596/hierarchy_entries/39151028/overview         
27 http://eol.org/pages/12096554/hierarchy_entries/39151075/overview         
28 http://eol.org/pages/12096563/hierarchy_entries/39151089/overview         
29     http://eol.org/pages/8228/hierarchy_entries/39151090/overview   superorder
30 http://eol.org/pages/12096677/hierarchy_entries/39151232/overview         
31  http://eol.org/pages/4656110/hierarchy_entries/39151366/overview         
32     http://eol.org/pages/5184/hierarchy_entries/39152344/overview        order
33  http://eol.org/pages/2793360/hierarchy_entries/39152345/overview     suborder
34     http://eol.org/pages/5258/hierarchy_entries/39153618/overview       family



eol_hierarchy(out[out$nameAccordingTo == "Integrated Taxonomic Information System (ITIS)", "identifier"])

http://www.eol.org/api/hierarchy_entries/1.0/46538152.json?common_names=1&synonyms=1

   sourceIdentifier  taxonID parentNameUsageID taxonConceptID  scientificName
1            202423 46216568                 0              1        Animalia
2            158852 46516964          46216568            694        Chordata
3            331030 46517559          46516964        2774383      Vertebrata
4            161030 46518910          46517559        2775704    Osteichthyes
5            161061 46518934          46518910           1905  Actinopterygii
6            553120 46518998          46518934        2775792     Neopterygii
7            161105 46519014          46518998        2775808       Teleostei
8            166082 46533001          46519014           8228 Acanthopterygii
9            167640 46536049          46533001           5184     Perciformes
10           167641 46536567          46536049        2793360       Percoidei
11           168557 46538151          46536567           5258     Pomatomidae
     taxonRank                                                           source
1      kingdom       http://eol.org/pages/1/hierarchy_entries/46216568/overview
2     division     http://eol.org/pages/694/hierarchy_entries/46516964/overview
3  subdivision http://eol.org/pages/2774383/hierarchy_entries/46517559/overview
4   superclass http://eol.org/pages/2775704/hierarchy_entries/46518910/overview
5        class    http://eol.org/pages/1905/hierarchy_entries/46518934/overview
6     subclass http://eol.org/pages/2775792/hierarchy_entries/46518998/overview
7   infraclass http://eol.org/pages/2775808/hierarchy_entries/46519014/overview
8   superorder    http://eol.org/pages/8228/hierarchy_entries/46533001/overview
9        order    http://eol.org/pages/5184/hierarchy_entries/46536049/overview
10    suborder http://eol.org/pages/2793360/hierarchy_entries/46536567/overview
11      family    http://eol.org/pages/5258/hierarchy_entries/46538151/overview