README.md

rinat: Access iNaturalist data with R

Edmund Hart, Stéphane Guillou

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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.

Installation

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")

Usage

Get observations

Text search

You can search for observations by either common or scientific name. It will search the entire iNaturalist database, so the search below will return all entries that mention Monarch butterflies, not just Monarch observations.

library(rinat)
monarchs <- get_inat_obs(query = "Monarch Butterfly")
unique(monarchs$scientific_name)
## [1] "Danaus plexippus" "Danaina"

Note that get_inat_obs() will return 100 observations by default. This can be controlled with the maxresults argument.

Another use for a fuzzy search is searching for a habitat, e.g. searching for all observations that might happen in a vernal pool. We can then see all the taxon names found.

vp_obs <- get_inat_obs(query = "vernal pool")
# see the first few taxa
head(vp_obs$scientific_name)
## [1] "Micrathetis triplex"     "Sphaeropthalma unicolor"
## [3] "Lepidoptera"             "Lepidoptera"            
## [5] "Synchlora faseolaria"    "Lepidoptera"

Taxon search

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:

nymphalidae <- get_inat_obs(taxon_name  = "Nymphalidae", year = 2015)
# how many unique taxa?
length(unique(nymphalidae$scientific_name))
## [1] 79

And to return only the Monarch butterfly observations that also mention the term “chrysalis”:

monarch_chrysalis <- get_inat_obs(taxon_name = "Danaus plexippus", query = "chrysalis")

Bounding box search

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)

Other functions

More functions are available, notably to access:

More detailed examples are included in the vignette:

vignette("rinat-intro", package = "rinat")

Mapping

Basic maps can be created as well to quickly visualize search results. Maps can either be plotted automatically with plot = TRUE (the default), or simply return a ggplot2 object with plot = FALSE. This works well with single species data, but more complicated plots are best made from scratch.

library(ggplot2)

## Map 100 spotted salamanders
a_mac <- get_inat_obs(taxon_name = "Ambystoma maculatum")
salamander_map <- inat_map(a_mac, plot = FALSE)

### Now we can modify the returned map
salamander_map + borders("state") + theme_bw()

inat_map() is useful for quickly mapping data obtained with rinat. Here is an example of customised map that does not make use of it. (Not 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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rinat documentation built on March 8, 2021, 5:06 p.m.