proxy.md

Install taxize

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

these apparently require user to pass in proxy auth details

tnrs

tnrs(query = c("Panthera tigris", "Neotamias minimus", "Magnifera indica"))

Calling http://taxosaurus.org/retrieve/a4f1a4dd934c6faf488e3e09ee7d671b
      submittedname     acceptedname    sourceid score       matchedname authority                                        uri
1  Magnifera indica Mangifera indica iPlant_TNRS  0.98  Mangifera indica        L.       http://www.tropicos.org/Name/1300071
2   Panthera tigris       Megalachne iPlant_TNRS  0.48        Pantathera    Steud.      http://www.tropicos.org/Name/40015658
3  Magnifera indica Mangifera indica        NCBI     1  Magnifera indica      none http://www.ncbi.nlm.nih.gov/taxonomy/29780
4   Panthera tigris  Panthera tigris        NCBI     1   Panthera tigris      none  http://www.ncbi.nlm.nih.gov/taxonomy/9694
5 Neotamias minimus   Tamias minimus        NCBI     1 Neotamias minimus      none http://www.ncbi.nlm.nih.gov/taxonomy/45468

gnr_resolve

gnr_resolve(names = c("Helianthus annuus", "Homo sapiens"), data_source_ids = 12)

$results
     submitted_name                matched_name data_source_title score
1 Helianthus annuus           Helianthus annuus               EOL 0.988
2 Helianthus annuus  Helianthus annuus Linnaeus               EOL 0.988
3 Helianthus annuus        Helianthus annuus L.               EOL 0.988
4 Helianthus annuus Helianthus annuus L. (1753)               EOL 0.988
5      Homo sapiens                Homo sapiens               EOL 0.988
6      Homo sapiens Homo sapiens Linnaeus, 1758               EOL 0.988
7      Homo sapiens             Homo sapiens L.               EOL 0.988

$preferred
NULL

these apparently DO NOT require user to pass in proxy auth details

classification

classification("Puma concolor", db = 'ncbi')

Retrieving data for taxon 'Puma concolor'

$`Puma concolor`
                   name         rank
1    cellular organisms      no rank
2             Eukaryota superkingdom
3          Opisthokonta      no rank
4               Metazoa      kingdom
5             Eumetazoa      no rank
6             Bilateria      no rank
7         Deuterostomia      no rank
8              Chordata       phylum
9              Craniata    subphylum
10           Vertebrata      no rank
11        Gnathostomata      no rank
12           Teleostomi      no rank
13         Euteleostomi      no rank
14        Sarcopterygii      no rank
15 Dipnotetrapodomorpha      no rank
16            Tetrapoda      no rank
17              Amniota      no rank
18             Mammalia        class
19               Theria      no rank
20             Eutheria      no rank
21        Boreoeutheria      no rank
22       Laurasiatheria   superorder
23            Carnivora        order
24           Feliformia     suborder
25              Felidae       family
26              Felinae    subfamily
27                 Puma        genus
28        Puma concolor      species

attr(,"class")
[1] "classification"
attr(,"db")
[1] "ncbi"

tax_name

tax_name(query = "Helianthus annuus", get = "family", db = "itis")

Retrieving data for taxon 'Helianthus annuus'

      family
1 Asteraceae