R wrapper for iNaturalist APIs for accessing the observations. The Detailed documentation of API is available on iNaturlaist website and is part of our larger species occurence searching packages SPOCC
Searching
Fuzzy search
You can search for observations by either common or latin name. It will search the entire iNaturalist entry, so the search below will return all entries that mention Monarch butterflies, not just entries for Monarchs.
library(rinat)
butterflies <- get_inat_obs(query = "Monarch Butterfly")
Another use for a fuzzy search is searching for a common name or habitat, e.g. searching for all observations that might happen in a vernal pool. We can then see all the species names found.
vp_obs <- get_inat_obs(query = "vernal pool")
head(vp_obs$species_guess)
## [1] "Eastern Hemlock" ""
## [3] "Longtail Tadpole Shrimp" "Great Blue Skimmer"
## [5] "Wood Frog" ""
Taxon query To return only records for a specific species or taxonomic group, use the taxon option.
## Return just observations in the family Plecoptera
stone_flies <- get_inat_obs(taxon_name = "Plecoptera", year = 2010)
## Return just Monarch Butterfly records
just_butterflies <- get_inat_obs(taxon_name = "Danaus plexippus")
Bounding box search
You can also search within a bounding box by giving a simple set of coordinates.
## Search by area
bounds <- c(38.44047, -125, 40.86652, -121.837)
deer <- get_inat_obs(query = "Mule Deer", bounds = bounds)
Other functions
Get information and observations by project
You can get all the observations for a project if you know it's ID or name as an intaturalist slug
## Just get info about a project
vt_crows <- get_inat_obs_project("crows-in-vermont", type = "info", raw = FALSE)
## 137 Records
## 0
## Now get all the observations for that project
vt_crows_obs <- get_inat_obs_project(vt_crows$id, type = "observations")
## 137 Records
## 0-100-200
Get observation details
Detailed information about a specific observation can be retrieved by observation ID. The easiest way to get the ID is from a more general search.
m_obs <- get_inat_obs(query = "Monarch Butterfly")
head(get_inat_obs_id(m_obs$id[1]))
## $id
## [1] 5209229
##
## $observed_on
## [1] "2016-12-12"
##
## $description
## NULL
##
## $latitude
## [1] "-42.9071542023"
##
## $longitude
## [1] "172.6419067383"
##
## $map_scale
## NULL
Get all observations by user
If you just want all the observations by a user you can download all their observations by user ID. A word of warning though, this can be quite large (easily into the 1000's)
m_obs <- get_inat_obs(query = "Monarch Butterfly")
head(get_inat_obs_user(as.character(m_obs$user_login[1]), maxresults = 20))[,1:5]
## scientific_name datetime
## 1 Vanessa itea 2016-12-12 12:33:00 +1300
## 2 Danaus plexippus 2016-12-12 12:30:00 +1300
## 3 Danaus plexippus 2016-12-12 11:53:00 +1300
## 4 Danaus plexippus 2016-12-12 11:52:00 +1300
## 5 Danaus plexippus 2016-12-12 11:41:00 +1300
## 6 Danaus plexippus 2016-12-12 11:43:00 +1300
## description
## 1
## 2
## 3
## 4
## 5
## 6 This Monarch appears to have slightly deformed wings.
## place_guess latitude
## 1 Hawarden, New Zealand -42.90615
## 2 Hawarden, New Zealand -42.90715
## 3 Hawarden, New Zealand -42.91621
## 4 Hawarden, New Zealand -42.90816
## 5 Hawarden, New Zealand -42.91319
## 6 NA
Stats by taxa
Basic statistics are available for taxa counts by date, date range, place ID (numeric ID), or user ID (string)
## By date
counts <- get_inat_taxon_stats(date = "2010-06-14")
print(counts$total)
## [1] 120
print(counts$species_counts[1:5,])
## count taxon.id taxon.name taxon.rank taxon.rank_level
## 1 5 57495 Melitaea cinxia species 10
## 2 2 17008 Sayornis phoebe species 10
## 3 2 52589 Coenonympha pamphilus species 10
## 4 2 55908 Lepus timidus species 10
## 5 2 56057 Leucanthemum vulgare species 10
## taxon.default_name.id taxon.default_name.name
## 1 91278 Glanville Fritillary
## 2 20369 Eastern Phoebe
## 3 114753 Small Heath
## 4 88688 Mountain Hare
## 5 89055 Ox-eye Daisy
## taxon.default_name.is_valid taxon.default_name.lexicon
## 1 TRUE English
## 2 TRUE English
## 3 TRUE English
## 4 TRUE English
## 5 TRUE English
## taxon.default_name.taxon_id taxon.default_name.created_at
## 1 57495 2010-03-17T07:57:02.000+01:00
## 2 17008 2008-03-13T04:33:20.000+01:00
## 3 52589 2011-05-05T21:50:31.000+02:00
## 4 55908 2010-02-11T17:05:42.000+01:00
## 5 56057 2010-02-16T22:05:51.000+01:00
## taxon.default_name.updated_at taxon.default_name.position
## 1 2010-03-17T07:57:02.000+01:00 0
## 2 2008-03-13T04:33:20.000+01:00 0
## 3 2011-05-05T21:50:31.000+02:00 0
## 4 2010-02-11T17:05:42.000+01:00 0
## 5 2017-01-05T00:57:29.655+01:00 0
## taxon.image_url
## 1 https://farm6.staticflickr.com/5206/5309980832_01c907d2f9_s.jpg
## 2 https://farm6.staticflickr.com/5009/5346970195_d0eac9966b_s.jpg
## 3 https://farm5.staticflickr.com/4005/4624300321_d1a46ff97e_s.jpg
## 4 https://farm6.staticflickr.com/5483/11718223795_b05531bbf6_s.jpg
## 5 https://static.inaturalist.org/photos/10419/square.jpg?1444278709
## taxon.iconic_taxon_name taxon.conservation_status_name
## 1 Insecta <NA>
## 2 Aves least_concern
## 3 Insecta <NA>
## 4 Mammalia least_concern
## 5 Plantae <NA>
print(counts$rank_counts)
## $species
## [1] 102
##
## $genus
## [1] 8
##
## $subspecies
## [1] 4
##
## $family
## [1] 2
##
## $variety
## [1] 2
##
## $order
## [1] 1
##
## $phylum
## [1] 1
Stats by user
Similar statistics can be gotten for users. The same input parameters can be used, but results are the top five users by species count and observation count.
## By date
counts <- get_inat_user_stats(date = "2010-06-14")
print(counts$total)
## [1] 61
print(counts$most_observations[1:10,])
## count user.id user.login user.name
## 1 12 357375 richardling Richard Ling
## 2 10 9706 greglasley Greg Lasley
## 3 8 109098 leannewallisbiologist
## 4 8 362446 pwdeacon
## 5 7 317332 mortenddhansen Morten DD Hansen
## 6 4 357 annetanne
## 7 4 3499 bryanto
## 8 4 10285 finatic BJ Stacey
## 9 3 382 tsoleau
## 10 3 873 tapbirds Scott Cox
## user.user_icon_url
## 1 https://static.inaturalist.org/attachments/users/icons/357375/thumb.jpg?1484462740
## 2 https://static.inaturalist.org/attachments/users/icons/9706/thumb.jpg?1475532223
## 3 https://static.inaturalist.org/attachments/users/icons/109098/thumb.jpg?1475547611
## 4 https://static.inaturalist.org/attachments/users/icons/362446/thumb.jpg?1478142809
## 5 https://static.inaturalist.org/attachments/users/icons/317332/thumb.jpeg?1475532800
## 6 https://static.inaturalist.org/attachments/users/icons/357/thumb.jpg?1475527524
## 7 https://static.inaturalist.org/attachments/users/icons/3499/thumb.jpg?1475528879
## 8 https://static.inaturalist.org/attachments/users/icons/10285/thumb.jpg?1475532519
## 9 https://static.inaturalist.org/attachments/users/icons/382/thumb.jpg?1475527539
## 10 https://static.inaturalist.org/attachments/users/icons/873/thumb.jpg?1475527722
print(counts$most_species[1:10,])
## count user.id user.login user.name
## 1 10 9706 greglasley Greg Lasley
## 2 10 357375 richardling Richard Ling
## 3 8 362446 pwdeacon
## 4 7 109098 leannewallisbiologist
## 5 4 10285 finatic BJ Stacey
## 6 3 382 tsoleau
## 7 3 3403 davidr David R
## 8 3 3499 bryanto
## 9 3 18056 plantman <NA>
## 10 3 38530 kevinhintsa
## user.user_icon_url
## 1 https://static.inaturalist.org/attachments/users/icons/9706/thumb.jpg?1475532223
## 2 https://static.inaturalist.org/attachments/users/icons/357375/thumb.jpg?1484462740
## 3 https://static.inaturalist.org/attachments/users/icons/362446/thumb.jpg?1478142809
## 4 https://static.inaturalist.org/attachments/users/icons/109098/thumb.jpg?1475547611
## 5 https://static.inaturalist.org/attachments/users/icons/10285/thumb.jpg?1475532519
## 6 https://static.inaturalist.org/attachments/users/icons/382/thumb.jpg?1475527539
## 7 https://static.inaturalist.org/attachments/users/icons/3403/thumb.jpg?1475528831
## 8 https://static.inaturalist.org/attachments/users/icons/3499/thumb.jpg?1475528879
## 9 <NA>
## 10 https://static.inaturalist.org/attachments/users/icons/38530/thumb.jpg?1475547495
## By place_ID
vt_crows <- get_inat_obs_project("crows-in-vermont", type = "info", raw = FALSE)
## 137 Records
## 0
place_counts <- get_inat_user_stats(place = vt_crows$place_id)
print(place_counts$total)
## [1] 1421
print(place_counts$most_observations[1:10,])
## count user.id user.login user.name
## 1 18329 12158 erikamitchell Erika Mitchell
## 2 15800 2179 charlie Charlie Hohn
## 3 8046 12610 susanelliott Susan Elliott
## 4 5924 12036 zaccota Zac Cota
## 5 4388 11792 kylejones Kyle Jones
## 6 4324 12045 larry522 Larry Clarfeld
## 7 4308 317 kpmcfarland Kent McFarland
## 8 3835 28921 rwp84 roy pilcher
## 9 3065 18303 marvelliott Marv Elliott
## 10 2761 12049 gaudettelaura Laura Gaudette
## user.user_icon_url
## 1 https://static.inaturalist.org/attachments/users/icons/12158/thumb.jpeg?1475533280
## 2 https://static.inaturalist.org/attachments/users/icons/2179/thumb.jpg?1475528361
## 3 https://static.inaturalist.org/attachments/users/icons/12610/thumb.jpg?1475533475
## 4 https://static.inaturalist.org/attachments/users/icons/12036/thumb.jpg?1475533232
## 5 https://static.inaturalist.org/attachments/users/icons/11792/thumb.jpg?1475533125
## 6 https://static.inaturalist.org/attachments/users/icons/12045/thumb.jpg?1475533238
## 7 https://static.inaturalist.org/attachments/users/icons/317/thumb.jpg?1475527502
## 8 https://static.inaturalist.org/attachments/users/icons/28921/thumb.jpg?1475542431
## 9 https://static.inaturalist.org/attachments/users/icons/18303/thumb.jpg?1475537232
## 10 https://static.inaturalist.org/attachments/users/icons/12049/thumb.jpg?1475533241
print(place_counts$most_species[1:10,])
## count user.id user.login user.name
## 1 1869 12158 erikamitchell Erika Mitchell
## 2 1833 12610 susanelliott Susan Elliott
## 3 1677 12045 larry522 Larry Clarfeld
## 4 1350 11792 kylejones Kyle Jones
## 5 1235 2179 charlie Charlie Hohn
## 6 1108 6624 joannerusso
## 7 1062 317 kpmcfarland Kent McFarland
## 8 998 12049 gaudettelaura Laura Gaudette
## 9 833 3847 rpayne Ron Payne
## 10 793 28921 rwp84 roy pilcher
## user.user_icon_url
## 1 https://static.inaturalist.org/attachments/users/icons/12158/thumb.jpeg?1475533280
## 2 https://static.inaturalist.org/attachments/users/icons/12610/thumb.jpg?1475533475
## 3 https://static.inaturalist.org/attachments/users/icons/12045/thumb.jpg?1475533238
## 4 https://static.inaturalist.org/attachments/users/icons/11792/thumb.jpg?1475533125
## 5 https://static.inaturalist.org/attachments/users/icons/2179/thumb.jpg?1475528361
## 6 https://static.inaturalist.org/attachments/users/icons/6624/thumb.jpg?1475530731
## 7 https://static.inaturalist.org/attachments/users/icons/317/thumb.jpg?1475527502
## 8 https://static.inaturalist.org/attachments/users/icons/12049/thumb.jpg?1475533241
## 9 https://static.inaturalist.org/attachments/users/icons/3847/thumb.jpg?1475529084
## 10 https://static.inaturalist.org/attachments/users/icons/28921/thumb.jpg?1475542431
Basic maps can be created as well to quickly visualize search results.
Maps can either be plotted automatically plot = TRUE 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 salamanders in the genuse Ambystoma
m_obs <- get_inat_obs(taxon_name = "Ambystoma maculatum")
salamander_map <- inat_map(m_obs, plot = FALSE)
### Now we can modify the returned map
salamander_map + borders("state") + theme_bw()
## Warning: Removed 2 rows containing missing values (geom_point).
