itis. taxize 0.0.3

Usage

itis(query, searchtype = NULL)

Arguments

query: Any common or scientific name (character), or taxonomic serial number (numeric). Can supply a single query or many.
searchtype: Specify one or more of ITIS API methods (see http://www.itis.gov/ws_description.html for more information on these methods): "getacceptednamesfromtsn","getanymatchcount","getcommentdetailfromtsn", "getcommonnamesfromtsn","getcoremetadatafromtsn","getcoveragefromtsn", "getcredibilityratingfromtsn","getcurrencyfromtsn","getdatedatafromtsn", "getexpertsfromtsn","getfullhierarchyfromtsn","getfullrecordfromtsn", "getgeographicdivisionsfromtsn","getglobalspeciescompletenessfromtsn", "gethierarchydownfromtsn","gethierarchyupfromtsn","getitistermsfromcommonname", "getitistermsfromscientificname","getjurisdictionaloriginfromtsn", "getkingdomnamefromtsn","getlsidfromtsn","getothersourcesfromtsn", "getparenttsnfromtsn","getpublicationsfromtsn","getreviewyearfromtsn", "getscientificnamefromtsn","getsynonymnamesfromtsn","gettaxonauthorshipfromtsn", "gettaxonomicranknamefromtsn","gettaxonomicusagefromtsn", "getunacceptabilityreasonfromtsn","searchbycommonname", "searchbycommonnamebeginswith","searchbycommonnameendswith","searchbyscientificname", "searchforanymatch","searchforanymatchpaged".

Value

A variety of results can be returned depending on the function called. If many queries or functions, or many of both, are provided, results will be returned in a list.

Description

Use any API method for the ITIS API.

Examples

# Search by scientific name, can abbreviate
itis(query="Quercus douglasii", searchtype="searchbyscientificname")
       combinedname   tsn
1 Quercus douglasii 19322


# Get the full taxonomic hierarchy for a taxon from the TSN
itis(36616, "getfullhierarchyfromtsn")
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=36616
        parentName parentTsn      rankName         taxonName    tsn
1                                  Kingdom           Plantae 202422
2          Plantae    202422    Subkingdom    Viridaeplantae 846492
3   Viridaeplantae    846492  Infrakingdom      Streptophyta 846494
4     Streptophyta    846494      Division      Tracheophyta 846496
5     Tracheophyta    846496   Subdivision   Spermatophytina 846504
6  Spermatophytina    846504 Infradivision      Angiospermae 846505
7     Angiospermae    846505         Class     Magnoliopsida  18063
8    Magnoliopsida     18063    Superorder         Asteranae 846535
9        Asteranae    846535         Order         Asterales  35419
10       Asterales     35419        Family        Asteraceae  35420
11      Asteraceae     35420         Genus        Helianthus  36611
12      Helianthus     36611       Species Helianthus annuus  36616


# Search by scientific name, then use a TSN to get its parent TSN
itis("Ursus", "searchbyscientificname")
                       combinedname    tsn
1                  Molophilus ursus 120819
2                             Ursus 180541
3                   Ursus maritimus 180542
4                      Ursus arctos 180543
5                  Ursus americanus 180544
6               Ursus arctos arctos 202383
7              Ursus arctos nelsoni 202384
8           Ursus arctos horribilis 202385
9            Ursus arctos pruinosus 202386
10      Ursus americanus americanus 202387
11        Ursus americanus luteolus 202388
12                   Ursus luteolus 203539
13            Ammopursus ohlingerae 508723
14  Senecio aureus var. intercursus 540550
15 Pachydesmus crassicutis incursus 571660
16                 Camponotus ursus 576500
17                   Pheidole ursus 581293
18                         Melursus 621775
19                 Melursus ursinus 621848
20                 Ursus thibetanus 621850
21     Ursus thibetanus gedrosianus 622030
22      Ursus thibetanus thibetanus 622052
23         Ursus arctos isabellinus 622068
24        Ursus maritimus maritimus 622083
25          Ursus maritimus marinus 622084
26            Pseudotropheus pursus 648889
27                 Megathymus ursus 706715
28         Megathymus ursus deserti 707377
29           Megathymus ursus ursus 707378
30          Megathymus ursus violae 707379
31           Isohypsibius saltursus 710708
32         Melursus ursinus ursinus 726969
33       Melursus ursinus inornatus 726970
34   Ursus americanus altifrontalis 726971
35       Ursus americanus amblyceps 726972
36  Ursus americanus californiensis 726973
37       Ursus americanus carlottae 726974
38      Ursus americanus cinnamomum 726975
39        Ursus americanus emmonsii 726976
40        Ursus americanus eremicus 726977
41      Ursus americanus floridanus 726978
42       Ursus americanus hamiltoni 726979
43        Ursus americanus kermodei 726980
44        Ursus americanus machetes 726981
45        Ursus americanus perniger 726982
46          Ursus americanus pugnax 726983
47      Ursus americanus vancouveri 726984
48          Ursus arctos alascensis 726985
49         Ursus arctos beringianus 726986
50        Ursus arctos californicus 726987
51            Ursus arctos collaris 726988
52           Ursus arctos crowtheri 726989
53               Ursus arctos dalli 726990
54                Ursus arctos gyas 726991
55            Ursus arctos lasiotus 726992
56        Ursus arctos middendorffi 726993
57           Ursus arctos sitkensis 726994
58        Ursus arctos stikeenensis 726995
59            Ursus arctos syriacus 726996
60      Ursus thibetanus formosanus 726997
61       Ursus thibetanus japonicus 726998
62         Ursus thibetanus laniger 726999
63      Ursus thibetanus mupinensis 727000
64       Ursus thibetanus ussuricus 727001
65                Podabrus excursus 834357
66          Acanthogonatus incursus 849781
67               Argyrodes incursus 852210
68                      Tinus ursus 890967
69               Xysticus concursus 892101

itis(203539, "getparenttsnfromtsn")
http://www.itis.gov/ITISWebService/services/ITISService/getParentTSNFromTSN?tsn=203539
  parentTsn    tsn
1           203539

itis(203539, "getsynonymnamesfromtsn") # no synonyms in this case
http://www.itis.gov/ITISWebService/services/ITISService/getSynonymNamesFromTSN?tsn=203539
     name    tsn
1 nomatch 203539


# Use multiple queries on one call to the function
itis(query=list(203539, 202420), searchtype="getsynonymnamesfromtsn")
http://www.itis.gov/ITISWebService/services/ITISService/getSynonymNamesFromTSN?tsn=203539
http://www.itis.gov/ITISWebService/services/ITISService/getSynonymNamesFromTSN?tsn=202420
      name    tsn
1  nomatch 203539
2 Bacteria 202420


# Use multiple ITIS functions
itis(203539, c("getsynonymnamesfromtsn","getcommonnamesfromtsn"))
http://www.itis.gov/ITISWebService/services/ITISService/getSynonymNamesFromTSN?tsn=203539
http://www.itis.gov/ITISWebService/services/ITISService/getCommonNamesFromTSN?tsn=203539
$getsynonymnamesfromtsn
$getsynonymnamesfromtsn$`203539`
     name    tsn
1 nomatch 203539


$getcommonnamesfromtsn
$getcommonnamesfromtsn$`203539`
[1] getcommonnamesfromtsn
<0 rows> (or 0-length row.names)




# Use multiple ITIS functions and multiple queries
itis(query=list(203539, 202420), searchtype=c("getsynonymnamesfromtsn","getcommonnamesfromtsn"))
http://www.itis.gov/ITISWebService/services/ITISService/getSynonymNamesFromTSN?tsn=203539
http://www.itis.gov/ITISWebService/services/ITISService/getSynonymNamesFromTSN?tsn=202420
http://www.itis.gov/ITISWebService/services/ITISService/getCommonNamesFromTSN?tsn=203539
http://www.itis.gov/ITISWebService/services/ITISService/getCommonNamesFromTSN?tsn=202420
$getsynonymnamesfromtsn
$getsynonymnamesfromtsn$`203539`
     name    tsn
1 nomatch 203539

$getsynonymnamesfromtsn$`202420`
      name    tsn
1 Bacteria 202420


$getcommonnamesfromtsn
$getcommonnamesfromtsn$`203539`
[1] getcommonnamesfromtsn
<0 rows> (or 0-length row.names)

$getcommonnamesfromtsn$`202420`
   comname    lang    tsn
1 monerans English 202420