taxize, v0.0.3

taxize does all things taxonomic in R. taxize hits lots of web APIs for taxonomy - if we don' have it, just let us know on our issues page.

About the package

We are developing taxize as a package to allow users to search over many websites for species names (scientific and common) and download up and downstream taxonomic hierarchical information - and many other things.

The functions in the package that hit a specific API have a prefix and suffix separated by an underscore. They follow the format of service_whatitdoes. For example, gnr_resolve uses the Global Names Resolver API to resolve species names. General functions in the package that don't hit a specific API don't have two words separated by an underscore, e.g., classification.

You need API keys for Encyclopedia of Life (EOL), the Universal Biological Indexer and Organizer (uBio), Tropicos, and Plantminer.

Installing taxize

A stable version is now available on CRAN.

# Stable version from CRAN
install.packages('taxize')
library(taxize)


# or install the development version from our GitHub repo.
install.packages('devtools')
library(devtools)
install_github('taxize_', 'ropensci')
library(taxize)

Phylomatic - get a phylogeny of plant species

library(doMC)
registerDoMC(cores=4)

# input the taxonomic names
taxa <- c("Poa annua", "Abies procera", "Helianthus annuus")

# fetch the tree - the formatting of names and higher taxonmy is done within the function
tree <- phylomatic_tree(taxa=taxa, get = 'POST', informat='newick', method = "phylomatic", storedtree = "R20120829", taxaformat = "slashpath", outformat = "newick", clean = "true")

# plot the tree
plot(tree)

Integrated Taxonomic Information Service (ITIS)

Search by term and search type (Note: TSN stands for Taxonomic Serial Number)

searchbyscientificname("Tardigrada")

          combinedname    tsn
1   Rotaria tardigrada  58274
2 Notommata tardigrada  58898
3  Pilargis tardigrada  65562
4           Tardigrada 155166
5     Heterotardigrada 155167
6     Arthrotardigrada 155168
7       Mesotardigrada 155358
8         Eutardigrada 155362
9  Scytodes tardigrada 866744

Show higher taxonomy for a given TSN

classification(685566, ID = "tsn")

      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         Amphibia 173420
5       Amphibia    173420     Order          Caudata 173584
6        Caudata    173584    Family   Plethodontidae 173631
7 Plethodontidae    173631 Subfamily   Plethodontinae 550197
8 Plethodontinae    550197     Genus        Plethodon 173648
9      Plethodon    173648   Species Plethodon asupak 685566

Get a TSN from a species name

tsn <- get_tsn(searchterm = "Quercus_douglasii", searchtype = "sciname")

# use classification with get_tsn together:
classification(tsn)

$`1`
        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           Rosanae 846548
9          Rosanae    846548         Order           Fagales  19273
10         Fagales     19273        Family          Fagaceae  19275
11        Fagaceae     19275         Genus           Quercus  19276
12         Quercus     19276       Species Quercus douglasii  19322

NCBI Taxonomy Browser

## Get Unique Identifier
uids <- get_uid(c("Chironomus riparius", "Chaetopteryx"))

## And retrieve classification
out <- classification(uids)
lapply(out, head)

[[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

[[2]]
       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

Global Names Resolver (GNR)

Get just id's and names of sources in a data.frame

tail(gnr_datasources(todf = T))

    id                                title
82 164                            BioLib.cz
83 165 Tropicos - Missouri Botanical Garden
84 166                                nlbif
85 167  The International Plant Names Index
86 168              Index to Organism Names
87 169                        uBio NameBank

Give me the id for EOL (Encyclopedia of Life)

out <- gnr_datasources(todf = T)
out[out$title == "EOL", "id"]

[1] 12

## Fuzzy search for sources with the word "zoo"
out <- gnr_datasources(todf = T)
outdf <- out[agrep("zoo", out$title, ignore.case = T), ]
outdf[1:2, ]

    id             title
20 100 Mushroom Observer
25 105           ZooKeys

Resolve some names

### Search for _Helianthus annuus_ and _Homo sapiens_, return a data.frame
gnr_resolve(names = c("Helianthus annuus", "Homo sapiens"), returndf = TRUE)[1:2, ]

  data_source_id    submitted_name       name_string score    title
1              4 Helianthus annuus Helianthus annuus 0.988     NCBI
3             10 Helianthus annuus Helianthus annuus 0.988 Freebase

### Search for the same species, with only using data source 12 (i.e., EOL)
gnr_resolve(names = c("Helianthus annuus", "Homo sapiens"), data_source_ids = "12", returndf = TRUE)

  data_source_id    submitted_name       name_string score title
1             12 Helianthus annuus Helianthus annuus 0.988   EOL
2             12      Homo sapiens      Homo sapiens 0.988   EOL

Tropicos

Get accepted names

head(tp_acceptednames(id = 25503923))

                   variable             value category
1                    NameId          25503923  Synonym
2            ScientificName       Aira pumila  Synonym
3 ScientificNameWithAuthors Aira pumila Pursh  Synonym
4                    Family           Poaceae  Synonym
5                    NameId          25509881 Accepted
6            ScientificName         Poa annua Accepted

Get synonyms

head(tp_synonyms(id = 25509881))

                   variable             value category
1                    NameId          25503923  Synonym
2            ScientificName       Aira pumila  Synonym
3 ScientificNameWithAuthors Aira pumila Pursh  Synonym
4                    Family           Poaceae  Synonym
5                    NameId          25509881 Accepted
6            ScientificName         Poa annua Accepted

uBio

Search uBio for elephant using ubio_namebank

ubio_namebank(searchName = "elephant", sci = 1, vern = 0)

  namebankID               nameString           fullNameString packageID packageName
1    6938660 Q2VyeWxvbiBlbGVwaGFudA== Q2VyeWxvbiBlbGVwaGFudA==        80 Cerylonidae
  basionymUnit rankID rankName
1      6938660     24  species

head(ubio_namebank(searchName = "Helianthus annuus", sci = 1, vern = 0)[,-c(2, 3)])

  namebankID packageID packageName basionymUnit rankID   rankName
1    2658020       598   Asterales            0     24    species
2     462478       598   Asterales            0     24    species
3    9073865      5634  Asteraceae            0    444         fo
4    9073864      5634  Asteraceae            0    444         fo
5    8624412      5634  Asteraceae      8722942    444         fo
6    8291505      5634  Asteraceae            0    265 subspecies

Search for two plant species

out <- lapply(list("Helianthus debilis", "Astragalus aduncus"), function(x) ubio_namebank(searchName = x, sci = 1, vern = 0))
head(out[[2]][, -c(2, 3)])  # just Astragalus aduncus output

  namebankID packageID packageName basionymUnit rankID rankName
1    2843601       663     Rosales            0     24  species
2    9261962      5780    Fabaceae            0    261       SP
3    9261999      5780    Fabaceae            0    261       SP
4    9261975      5780    Fabaceae            0    261       SP
5     704148       663     Rosales            0     24  species
6    8374424      5780    Fabaceae       722833    444       fo

IUCN Red List

Query the Red List API

ia <- iucn_summary(c("Panthera uncia", "Lynx lynx"))

Extract Status

library(plyr)
laply(ia, function(x) x$status)

[1] "EN" "LC"

Support and Bugs

For bugs, feature requests and other issues, please submit an issue via Github.

For general comments, email scott at ropensci.gmail.com . This package is part of the rOpenSci suite of R tools. For similar packages visit ropensci.org

License

This work is licensed under a Creative Commons Attribution 3.0 Unported License.