knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
Access and download data on plant and animal populations from various databases through NatureCounts, a service managed by Birds Canada.
See tutorials, documentation and articles on the naturecounts package Website
You can install the main version of naturecounts
from our R-Universe
install.packages("naturecounts", repos = c(birdscanada = 'https://birdscanada.r-universe.dev', CRAN = 'https://cloud.r-project.org'))
library(naturecounts)
Use the nc_count()
function to return collections and the number of observations in each for which you have access (here returns all collections associated with username sample).
nc_count(username = "sample")
Use the show = "all"
argument to show counts for all collections available (public or otherwise).
nc_count(show = "all") %>% head()
Fetch all observations of bittern which are available to user sample into a local data frame.
First find the species id
search_species("American Bittern")
Use this id with nc_data_dl()
. The info
parameter is a short description of what the data is being downloaded for.
bittern <- nc_data_dl(species = 2490, username = "sample", info = "readme_example")
Alternatively, save the downloaded data as a SQLite database (bittern
).
bittern <- nc_data_dl(species = 2490, sql_db = "bittern", username = "sample", info = "readme_example")
file.remove("bittern.nc")
To access private/semi-public projects/collections you must sign up for a free NatureCounts account and register for the projects you'd like to access. Once registered, you can use the username
argument (you will be prompted for a password) for both nc_count()
and nc_data_dl()
, which will then return a different set of records.
nc_count(username = "my_user_name") bittern <- nc_data_dl(species = 2490, username = "my_user_name", info = "readme_example")
nc_count()
and nc_data_dl()
have a variety of arguments that allow you to filter the counts/data prior to downloading. These options include collections
, species
, years
, doy
(day-of-year), region
, and site_type
(users can specify up to 3 of these). For nc_data_dl()
you have the additional arguments fields_set
and fields
with which you can customize which fields/columns to include in your download.
See the function examples (nc_count()
, nc_data_dl()
) the following articles for more information on these filters:
We also have an article on post-filtering your data
NatureCounts includes a great deal of metadata which can be accessed through the functions with the meta_
prefix. See the Meta Documentation for specifics.
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