rnpn: An R interface for the National Phenology Network

August 31, 2011
By

(This article was first published on Recology, and kindly contributed to R-bloggers)

The team at rOpenSci and I have been working on a wrapper for the USA National Phenology Network API. The following is a demo of some of the current possibilities. We will have more functions down the road. Get the publicly available code, and contribute, at Github here. If you try this out look at the Description file for the required R packages to run rnpn. Let us know at Github or at http://ropensci.org/, or in the comments below, or on twitter (@rOpenSci), what use cases you would like to see with the rnpn package.

Method and demo of each:
Get observations for species by day
From the documentation: "This function will return a list of species, containing all the dates which observations were made about the species, and a count of the number of such observations made on that date."

#### Note, the data below is truncated for blogging brevity...
> getobsspbyday(c(1, 2), '2008-01-01', '2011-12-31') # Searched for species 1 and 2 from Jan 1, 2008 to Dec 31, 2011

date count species
1 2009-03-08 2 species 1
2 2009-03-15 1 species 1
3 2009-03-22 1 species 1
4 2009-03-24 1 species 1
5 2009-03-26 1 species 1
6 2009-04-17 1 species 1
7 2009-04-24 1 species 1
8 2009-05-12 1 species 1
9 2009-05-20 1 species 1
10 2009-11-24 1 species 1
11 2009-12-07 1 species 1
12 2010-01-18 1 species 1
13 2010-01-23 1 species 1
62 2011-05-29 1 species 1
63 2011-06-27 1 species 1
64 2011-06-30 2 species 1
65 2009-03-17 1 species 2
66 2009-04-03 3 species 2
67 2009-04-05 3 species 2
68 2009-04-10 3 species 2
69 2009-04-17 3 species 2






Get individuals at specific stations
From the documentation: "This function returns all of the individuals at a series of stations."

> getindsatstations(c(507, 523)) # Searched for any individuals at stations 507 and 523

individual_id individual_name species_id kingdom
1 1200 dogwood 12 Plantae
2 1197 purple lilac 36 Plantae
3 1193 white t 38 Plantae
4 3569 forsythia-1 73 Plantae
5 1206 jack 150 Plantae
6 1199 trout lily 161 Plantae
7 1198 dandy 189 Plantae
8 1192 red t 192 Plantae
9 1710 common lilac 36 Plantae
10 1711 common lilac 2 36 Plantae
11 1712 dandelion 189 Plantae







Get individuals of species at stations
From the documentation: "This function will return a list of all the individuals, which are members of a species, among  any number of stations."

> getindspatstations(35, c(60, 259), 2009)  # Search for individuals of species 35 at stations 60 and 259 in year 2009

individual_id individual_name number_observations
1 1715 west 5
2 1716 east 5









Get observation associated with particular observation
From the documentation: "This function will return the comment associated with a particular observation."

> getobscomm(1938) # The observation for observation number 1938
$observation_comment

[1] "some lower branches are bare"

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