taxize changes

We are building a taxonomic toolbelt for R called taxize - which gives you programmatic access to many sources of taxonomic data on the web. We just pushed a new version to CRAN (v0.1.5) with a lot of changes (see here for a rundown). Here are a few highlights of the changes.

Note: the windows binary may not be available yet...


Install and load taxize

install.packages("taxize")
library(taxize)

Taxonomic identifiers

Each taxonomic service has their own unique ID for a taxon. We had a way to get ITIS and NCBI identifiers before - we now have functions for Tropicos, EOL, and the Catalogue of Life.

get_tpsid(sciname = "Helianthus petiolaris patens")
##        1
## 50140022
## attr(,"class")
## [1] "tpsid"
get_colid(sciname = "Pinus contorta")
##          1
## "14376216"
## attr(,"class")
## [1] "colid"

And we have a new function to get identifiers across all sources. And it's vectorized so you can pass in many names.

get_ids(names = c("Chironomus riparius", "Poa annua"), db = c("ncbi", "itis"))
## $ncbi
## Chironomus riparius           Poa annua
##            "315576"             "93036"
## attr(,"match")
## [1] "found" "found"
## attr(,"class")
## [1] "uid"
##
## $itis
## Chironomus riparius           Poa annua
##            "129313"             "41107"
## attr(,"match")
## [1] "found" "found"
## attr(,"class")
## [1] "tsn"
##
## attr(,"class")
## [1] "ids"

Taxonomic classifications

We had a function called classification to get a taxonomic hierarchy from a particular source, ITIS or NCBI. We now have functions for Tropicos, EOL, and the Catalogue of Life. In addition, we have a function to get classifications across sources.

out <- get_ids(names = "Poa annua", db = c("ncbi", "itis"))
classification(out)
## $ncbi
## $ncbi$`Poa annua`
##        ScientificName         Rank    UID
## 1  cellular organisms      no rank 131567
## 2           Eukaryota superkingdom   2759
## 3       Viridiplantae      kingdom  33090
## 4        Streptophyta       phylum  35493
## 5      Streptophytina      no rank 131221
## 6         Embryophyta      no rank   3193
## 7        Tracheophyta      no rank  58023
## 8       Euphyllophyta      no rank  78536
## 9       Spermatophyta      no rank  58024
## 10      Magnoliophyta      no rank   3398
## 11         Liliopsida        class   4447
## 12        commelinids     subclass   4734
## 13             Poales        order  38820
## 14            Poaceae       family   4479
## 15          BEP clade      no rank 359160
## 16           Pooideae    subfamily 147368
## 17              Poeae        tribe 147387
## 18             Poinae     subtribe 640628
## 19                Poa        genus   4544
## 20          Poa annua      species  93036
##
##
## $itis
## $itis$`Poa annua`
##         rankName       taxonName    tsn
## 1        Kingdom         Plantae 202422
## 2     Subkingdom  Viridaeplantae 846492
## 3   Infrakingdom    Streptophyta 846494
## 4       Division    Tracheophyta 846496
## 5    Subdivision Spermatophytina 846504
## 6  Infradivision    Angiospermae 846505
## 7          Class   Magnoliopsida  18063
## 8     Superorder        Lilianae 846542
## 9          Order          Poales 846620
## 10        Family         Poaceae  40351
## 11         Genus             Poa  41074
## 12       Species       Poa annua  41107

Synonyms

Just like the classification function, synonyms now searches across sources for synonym names. However, this function only has methods for ITIS and Tropicos.

synonyms(c("Poa annua", "Pinus contorta", "Puma concolor"), db = "itis")
## $`Poa annua`
##                           name    tsn
## 1      Poa annua var. aquatica 538978
## 2       Poa annua var. reptans 538979
## 3                  Aira pumila 785854
## 4             Catabrosa pumila 787993
## 5               Ochlopoa annua 791574
## 6               Poa aestivalis 793946
## 7                   Poa algida 793954
## 8         Poa annua var. annua 802116
## 9     Poa annua var. eriolepis 802117
## 10 Poa annua var. rigidiuscula 802119
## 11        Poa annua f. reptans 803667
##
## $`Pinus contorta`
##      name    tsn
## 1 nomatch 183327
##
## $`Puma concolor`
##             name    tsn
## 1 Felis concolor 180587

Common names from scientific names and vice versa

We have a variety of ways to get common names from scientific names for different sources. To simply things, there are two new functions to work across sources.

sci2comm(scinames = "Helianthus annuus", db = "itis")
## $`Helianthus annuus`
##            comname    lang   tsn
## 1 common sunflower English 36616
## 2        sunflower English 36616
## 3   wild sunflower English 36616
## 4 annual sunflower English 36616

And vice versa

comm2sci(commnames = "annual blue grass", db = "tropicos")
## $`annual blue grass`
##     NameId ScientificName ScientificNameWithAuthors  Family
## 1 25509881      Poa annua              Poa annua L. Poaceae
##   RankAbbreviation NomenclatureStatusID NomenclatureStatusName Symbol
## 1              sp.                    1             Legitimate      !
##   Author DisplayReference DisplayDate TotalRows
## 1     L.    Sp. Pl. 1: 68        1753         1

ITIS functions

We reworked the functions that interact with the ITIS service. We still have all the same functions, but there are now a number of higher level functions that make the interface to ITIS simpler. Here are some examples:

Get references associated with names.

itis_refs(c(202385, 70340))
## [[1]]
##   actualPubDate          isbn issn listedPubDate        pages
## 1    2005-10-01 0-8018-8221-4         2005-10-01         2142
## 2    1993-01-01 1-56098-217-9         1992-01-01 xviii + 1207
## 3    1981-04-03                       1981-04-03         1181
##                                      pubComment
## 1
## 2 Corrections were made to text at 3rd printing
## 3
##                                                                                    pubName
## 1  Mammal Species of the World: A Taxonomic and Geographic Reference, 3rd ed., vols. 1 & 2
## 2 Mammal Species of the World: A Taxonomic and Geographic Reference, 2nd ed., 3rd printing
## 3                                    The Mammals of North America, vols. I and II, 2nd ed.
##                   pubPlace                      publisher
## 1 Baltimore, Maryland, USA Johns Hopkins University Press
## 2      Washington, DC, USA  Smithsonian Institution Press
## 3  New York, New York, USA      John Wiley and Sons, Inc.
##                              referenceAuthor                    name
## 1 Wilson, Don E., and DeeAnn M. Reeder, eds. Ursus arctos horribilis
## 2 Wilson, Don E., and DeeAnn M. Reeder, eds. Ursus arctos horribilis
## 3                           Hall, E. Raymond Ursus arctos horribilis
##   refLanguage referredTsn title updateDate
## 1                  202385       2013-11-04
## 2                  202385       2013-11-04
## 3                  202385       2013-11-04
##
## [[2]]
##   actualPubDate          isbn      issn listedPubDate     pages pubComment
## 1    1988-01-01 0-913235-47-4 0097-0638    1988-01-01 vii + 277
## 2    1998-01-01 1-888569-01-8 0097-0638    1998-01-01       526
##                                             pubName
## 1 American Fisheries Society Special Publication 16
## 2 American Fisheries Society Special Publication 26
##                  pubPlace                  publisher
## 1 Bethesda, Maryland, USA American Fisheries Society
## 2 Bethesda, Maryland, USA American Fisheries Society
##                                                                                  referenceAuthor
## 1          Turgeon, D. D., A. E. Bogan, E. V. Coan, W. K. Emerson, W. G. Lyons, W. Pratt, et al.
## 2 Turgeon, D. D., J. F. Quinn, Jr., A. E. Bogan, E. V. Coan, F. G. Hochberg, W. G. Lyons, et al.
##                 name refLanguage referredTsn
## 1 Tulotoma magnifica                   70340
## 2 Tulotoma magnifica                   70340
##                                                                                                       title
## 1          Common and scientific names of aquatic invertebrates from the United States and Canada: mollusks
## 2 Common and scientific names of aquatic invertebrates from the United States and Canada: Mollusks, 2nd ed.
##   updateDate
## 1 2013-04-26
## 2 2013-11-04

Get hierarchy: full, up (immediate), and down (immediate)

itis_hierarchy(tsn = 180543)
##       parentName parentTsn     rankName                 taxonName    tsn
## 1                               Kingdom                  Animalia 202423
## 2       Animalia    202423   Subkingdom                 Bilateria 914154
## 3      Bilateria    914154 Infrakingdom             Deuterostomia 914156
## 4  Deuterostomia    914156       Phylum                  Chordata 158852
## 5       Chordata    158852    Subphylum                Vertebrata 331030
## 6     Vertebrata    331030  Infraphylum             Gnathostomata 914179
## 7  Gnathostomata    914179   Superclass                 Tetrapoda 914181
## 8      Tetrapoda    914181        Class                  Mammalia 179913
## 9       Mammalia    179913     Subclass                    Theria 179916
## 10        Theria    179916   Infraclass                  Eutheria 179925
## 11      Eutheria    179925        Order                 Carnivora 180539
## 12     Carnivora    180539     Suborder                Caniformia 552303
## 13    Caniformia    552303       Family                   Ursidae 180540
## 14       Ursidae    180540        Genus                     Ursus 180541
## 15         Ursus    180541      Species              Ursus arctos 180543
## 16  Ursus arctos    180543   Subspecies   Ursus arctos alascensis 726985
## 17  Ursus arctos    180543   Subspecies       Ursus arctos arctos 202383
## 18  Ursus arctos    180543   Subspecies  Ursus arctos beringianus 726986
## 19  Ursus arctos    180543   Subspecies Ursus arctos californicus 726987
## 20  Ursus arctos    180543   Subspecies     Ursus arctos collaris 726988
## 21  Ursus arctos    180543   Subspecies    Ursus arctos crowtheri 726989
## 22  Ursus arctos    180543   Subspecies        Ursus arctos dalli 726990
## 23  Ursus arctos    180543   Subspecies         Ursus arctos gyas 726991
## 24  Ursus arctos    180543   Subspecies   Ursus arctos horribilis 202385
## 25  Ursus arctos    180543   Subspecies  Ursus arctos isabellinus 622068
## 26  Ursus arctos    180543   Subspecies     Ursus arctos lasiotus 726992
## 27  Ursus arctos    180543   Subspecies Ursus arctos middendorffi 726993
## 28  Ursus arctos    180543   Subspecies    Ursus arctos pruinosus 202386
## 29  Ursus arctos    180543   Subspecies    Ursus arctos sitkensis 726994
## 30  Ursus arctos    180543   Subspecies Ursus arctos stikeenensis 726995
## 31  Ursus arctos    180543   Subspecies     Ursus arctos syriacus 726996
itis_hierarchy(tsn = 180543, what = "up")
##   parentName parentTsn rankName    taxonName    tsn
## 1      Ursus    180541  Species Ursus arctos 180543
itis_hierarchy(tsn = 180543, what = "down")
##      parentName parentTsn   rankName                 taxonName    tsn
## 1  Ursus arctos    180543 Subspecies       Ursus arctos arctos 202383
## 2  Ursus arctos    180543 Subspecies   Ursus arctos horribilis 202385
## 3  Ursus arctos    180543 Subspecies    Ursus arctos pruinosus 202386
## 4  Ursus arctos    180543 Subspecies  Ursus arctos isabellinus 622068
## 5  Ursus arctos    180543 Subspecies   Ursus arctos alascensis 726985
## 6  Ursus arctos    180543 Subspecies  Ursus arctos beringianus 726986
## 7  Ursus arctos    180543 Subspecies Ursus arctos californicus 726987
## 8  Ursus arctos    180543 Subspecies     Ursus arctos collaris 726988
## 9  Ursus arctos    180543 Subspecies    Ursus arctos crowtheri 726989
## 10 Ursus arctos    180543 Subspecies        Ursus arctos dalli 726990
## 11 Ursus arctos    180543 Subspecies         Ursus arctos gyas 726991
## 12 Ursus arctos    180543 Subspecies     Ursus arctos lasiotus 726992
## 13 Ursus arctos    180543 Subspecies Ursus arctos middendorffi 726993
## 14 Ursus arctos    180543 Subspecies    Ursus arctos sitkensis 726994
## 15 Ursus arctos    180543 Subspecies Ursus arctos stikeenensis 726995
## 16 Ursus arctos    180543 Subspecies     Ursus arctos syriacus 726996
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