Edmund Hart, Stéphane Guillou
R wrapper for iNaturalist APIs for accessing the observations. The detailed documentation of the API is available on the iNaturalist website and is part of our larger species occurrence searching packages SPOCC.
You can install the latest version available on CRAN with:
install.packages("rinat")Alternatively, you can install the development version from Github with:
remotes::install_github("ropensci/rinat")get_inat_obs() is the primary function that retrieves observations
from iNaturalist. The text or taxon search can be refined by observation
date, record quality and location.
It is recommended to set the
qualityargument to"research"in order to get more reliable data that has been validated by several contributors.
To return only records of a specific species or taxonomic group, use the
taxon_name argument. For example, to return observations of anything
from the Nymphalidae family, and restricting the search to the year
2015:
library(rinat)
nymphalidae <- get_inat_obs(taxon_name = "Nymphalidae", year = 2015)
# how many unique taxa?
length(unique(nymphalidae$scientific_name))## [1] 72
Note that
get_inat_obs()will return 100 observations by default. This can be controlled with themaxresultsargument.
You can also search observations with any string. It will search the entire iNaturalist database, so the search below will return all entries that mention Monarch butterflies, not just Monarch observations.
monarchs <- get_inat_obs(query = "Monarch Butterfly", year = 2021)
# which taxa were returned?
unique(monarchs$scientific_name)## [1] "Danaus plexippus" "Danaina"
You can combine the fuzzy search with the precise taxon search. For example, to get Monarch butterfly observations that also mention the term “chrysalis”:
monarch_chrysalis <- get_inat_obs(taxon_name = "Danaus plexippus", query = "chrysalis")You can also search within a bounding box by giving a simple set of coordinates.
## Search by area
bounds <- c(38.44047, -125, 40.86652, -121.837)
deer <- get_inat_obs(query = "Mule Deer", bounds = bounds)
plot(deer$longitude, deer$latitude)
More functions are available, notably to access:
- observations in a project with
get_inat_obs_project() - details of a single observation with
get_inat_obs_id() - observations from a single user with
get_inat_obs_user() - taxa statistics with
get_inat_taxon_stats() - user statistics with
get_inat_user_stats()
More detailed examples are included in the vignette:
vignette("rinat-intro", package = "rinat")Basic maps can be created with the inat_map() function to quickly
visualize search results. The plot = FALSE option can be used to avoid
displaying the initial plot when further customising it with ggplot2
functions.
library(ggplot2)
## Map 100 spotted salamanders
a_mac <- get_inat_obs(taxon_name = "Ambystoma maculatum", year = 2021)
salamander_map <- inat_map(a_mac, plot = FALSE)
### Further customise the returned ggplot object
salamander_map + borders("state") + theme_bw()
inat_map() is useful for quickly mapping single-species data obtained
with rinat. However, more complicated plots are best made from scratch.
Here is an example of customised map that does not make use of it. (Note
the use of quality = "research" to restrict the search to the more
reliable observations.)
## A more elaborate map of Colibri sp.
colibri <- get_inat_obs(taxon_name = "Colibri",
quality = "research",
maxresults = 500)
ggplot(data = colibri, aes(x = longitude,
y = latitude,
colour = scientific_name)) +
geom_polygon(data = map_data("world"),
aes(x = long, y = lat, group = group),
fill = "grey95",
color = "gray40",
size = 0.1) +
geom_point(size = 0.7, alpha = 0.5) +
coord_fixed(xlim = range(colibri$longitude, na.rm = TRUE),
ylim = range(colibri$latitude, na.rm = TRUE)) +
theme_bw()
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