R client for the National Phenology Network database API
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README.md

rnpn

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rnpn is an R client for the US National Phenology Network API.

National Phenology Network API documentation.

Note that there is no need for an API key to grab data from the National Phenology Network, but I think there is for writing data through the API. Currently, functions in this package only allow getting data, but may at some point allow posting data to the USNPN.

Installation

Stable version

install.packages("rnpn")

Development version

devtools::install_github("ropensci/rnpn")
library('rnpn')

Lookup names

You can lookup taxon names. This is not actually an API call to the web. The function simply searches for matches in a dataset stored in the package. You can then use the speciesid output in other functions.

lookup_names(name = 'Pinus', type = 'genus')
#>     species_id                  common_name genus    epithet itis_tsn
#> 82         967                  Bishop pine Pinus   muricata   183359
#> 312         53           eastern white pine Pinus    strobus   183385
#> 370        219 Great Basin bristlecone pine Pinus   longaeva   183352
#> 458        220                  limber pine Pinus   flexilis   183343
#> 461         54                loblolly pine Pinus      taeda    18037
#> 462        762               lodgepole pine Pinus   contorta   183327
#> 465         52                longleaf pine Pinus  palustris    18038
#> 479        965               Mexican pinyon Pinus cembroides   183321
#> 584         25               ponderosa pine Pinus  ponderosa   183365
#> 618        968                     red pine Pinus   resinosa   183375
#> 698         51            singleleaf pinyon Pinus monophylla   183353
#> 704        295                   slash pine Pinus  elliottii    18036
#> 794         50             twoneedle pinyon Pinus     edulis   183336
#> 836        966           western white pine Pinus  monticola   183356
#>        genus_epithet
#> 82    Pinus muricata
#> 312    Pinus strobus
#> 370   Pinus longaeva
#> 458   Pinus flexilis
#> 461      Pinus taeda
#> 462   Pinus contorta
#> 465  Pinus palustris
#> 479 Pinus cembroides
#> 584  Pinus ponderosa
#> 618   Pinus resinosa
#> 698 Pinus monophylla
#> 704  Pinus elliottii
#> 794     Pinus edulis
#> 836  Pinus monticola

Search

Search for a single species, specifying a start and end date. You can also pass a vector to the speciesid parameter.

npn_allobssp(speciesid = 52, startdate = '2008-01-01', enddate = '2010-12-31')
#> $taxa
#>     species_id genus   epithet   genus_epithet
#> 465         52 Pinus palustris Pinus palustris
#> 
#> $stations
#>   station_id           station_name  latitude  longitude
#> 1       4881 Possum Branch Preserve 28.045185 -82.706299
#> 
#> $phenophase
#>   phenophase_id      phenophase_name
#> 1           221 Full pollen release 
#> 2           393      Ripe seed cones
#> 3           486       Young needles 
#> 4           496    Emerging needles 
#> 5           503      Pollen release 
#> 
#> $data
#> $data$`4881`
#> $data$`4881`$`52`
#>    id  n  y
#> 1 221 39 NA
#> 2 393 17 23
#> 3 486 40 NA
#> 4 496 40 NA
#> 5 503 40 NA

List stations with xyz

Get a list of all stations which have an individual whom is a member of a set of species.

head( npn_stationswithspp(speciesid = 53) )
#>    latitude  longitude      station_name station_id
#> 1 44.340950 -72.461220  Frizzle Mountain        637
#> 2 42.176537 -85.892448              Home       1447
#> 3 44.588772 -93.004623              home       1572
#> 4 48.051636 -92.766304   Wolfhaunt Creek       1598
#> 5 48.051586 -92.764305 Wolfhaunt Prairie       1599
#> 6 39.973316 -82.802826              Home       1841

Stations by state

Number of stations by state.

head( npn_stationsbystate() )
#>   state number_stations
#> 1    CA            1935
#> 2    ME             902
#> 3    VA             833
#> 4    AZ             804
#> 5    MN             793
#> 6    CO             777

Observations by day

Get observations by day for a particular species or set of species.

library('plyr')
temp <- lookup_names(name = 'bird', type = 'common')
comnames <- as.character(temp[temp$species_id %in% c(357, 359, 1108), 'common_name'])

out <- npn_obsspbyday(speciesid = c(357, 359, 1108), startdate = '2010-04-01', enddate = '2013-09-31')
names(out) <- comnames
df <- ldply(out)
df$date <- as.Date(df$date)

library('ggplot2')
ggplot(df, aes(date, count)) +
 geom_line() +
 theme_grey(base_size = 20) +
 facet_grid(.id ~ .)

plot of chunk unnamed-chunk-9

Search for species

All species

head( npn_species() )
#>   species_id                 common_name        genus      species
#> 1        120                'ohi'a lehua Metrosideros   polymorpha
#> 2       1436                  absinthium    Artemisia   absinthium
#> 3       1227          Acadian flycatcher    Empidonax    virescens
#> 4       1229            acorn woodpecker   Melanerpes formicivorus
#> 5       1343 alderleaf mountain-mahogany  Cercocarpus     montanus
#> 6        174                     alfalfa     Medicago       sativa
#>   itis_taxonomic_sn
#> 1             27259
#> 2             35445
#> 3            178339
#> 4            178189
#> 5             25136
#> 6            183623

By ITIS taxonomic serial number

npn_species_itis(ids = 27806)
#>         common_name  genus species species_id
#> 1 flowering dogwood Cornus florida         12

By USNPN id

npn_species_id(ids = 3)
#>   common_name genus species itis_taxonomic_sn
#> 1   red maple  Acer  rubrum             28728

By state (and optionally kingdom)

head( npn_species_state(state = "HI", kingdom = "Plantae") )
#>   species_id       common_name        genus        species
#> 1        120      'ohi'a lehua Metrosideros     polymorpha
#> 2        174           alfalfa     Medicago         sativa
#> 3        145    annual ragweed     Ambrosia artemisiifolia
#> 4        124           avocado       Persea      americana
#> 5        898           bayhops      Ipomoea     pes-caprae
#> 6        870 beach strawberry      Fragaria     chiloensis
#>   itis_taxonomic_sn
#> 1             27259
#> 2            183623
#> 3             36496
#> 4             18154
#> 5             30787
#> 6             24625

By scientific name

npn_species_sci(genus = "Clintonia", species = "borealis")
#>   common_name itis_taxonomic_sn species_id
#> 1    bluebead             42903          9

By common name

npn_species_comm(name = "thickleaved wild strawberry")
#>      genus itis_taxonomic_sn    species species_id
#> 1 Fragaria             24639 virginiana         17

Filter by network, group, year, or station

head( npn_species_search(groups = 3, year = 2010) )
#>                common_name      genus        species species_id
#> 1                  alfalfa   Medicago         sativa        174
#> 2    alpine mountainsorrel     Oxyria         digyna        951
#> 3        American pokeweed Phytolacca      americana        963
#> 4    American skunkcabbage Lysichiton     americanus        922
#> 5 American white waterlily   Nymphaea        odorata        938
#> 6           annual ragweed   Ambrosia artemisiifolia        145
#>   number_observations
#> 1                5599
#> 2                   7
#> 3                 779
#> 4                 880
#> 5                  28
#> 6                1800

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for rnpn in R doing citation(package = 'rnpn')
  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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