rinat v0.1.6

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Access 'iNaturalist' Data Through APIs

A programmatic interface to the API provided by the 'iNaturalist' website <https://www.inaturalist.org/> to download species occurrence data submitted by citizen scientists.

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rinat: Access iNaturalist data with R

Edmund Hart, Stéphane Guillou

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status codecov.io

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

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"

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")

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:

  • 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")

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()


Functions in rinat

Name Description
get_inat_taxon_stats Get stats on taxon counts
get_inat_obs_project Download observations or info from a project
get_inat_obs_id Get information on a specific observation
get_inat_obs_user Download observations for a user
inat_map Plot iNaturalist observations
get_inat_user_stats Get stats on users
get_inat_obs Download iNaturalist data
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Vignettes of rinat

Name
rinat-intro.Rmd
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Details

Type Package
Date 2020-10-13
License MIT + file LICENSE
RoxygenNote 7.1.1
URL https://docs.ropensci.org/rinat/ (website) https://github.com/ropensci/rinat (devel)
VignetteBuilder knitr
Encoding UTF-8
NeedsCompilation no
Packaged 2020-10-13 14:06:15 UTC; stragu
Repository CRAN
Date/Publication 2020-10-14 09:10:03 UTC

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