In this Notebook, we’ll learn how to import observations from iNaturalist using the rinat package.
The first step is to load the packages we’ll need. These are all on CRAN if you need to install any.
library(rinat)
library(sf)
library(dplyr)
library(tmap)
library(leaflet)
## Load the conflicted package and set preferences
library(conflicted)
conflict_prefer("filter", "dplyr", quiet = TRUE)
conflict_prefer("count", "dplyr", quiet = TRUE)
conflict_prefer("select", "dplyr", quiet = TRUE)
conflict_prefer("arrange", "dplyr", quiet = TRUE)Next, we import the boundary of Yosemite and grab its bounding box. We’ll use this later when we call iNaturalist to specify that we’re we’re only interested in observations in this area.
## Import the YNP Boundary
yose_bnd_ll <- sf::st_read(dsn="./data", layer="yose_boundary")Reading layer `yose_boundary' from data source
`D:\Workshops\R-Spatial\rspatial_mod\outputs\rspatial_scgis23\exercises\data' using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 11 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: -119.8864 ymin: 37.4947 xmax: -119.1964 ymax: 38.18515
Geodetic CRS: North_American_Datum_1983## Get the bounding box
yose_bnd_bb <- st_bbox(yose_bnd_ll)
as.numeric(yose_bnd_bb)[1] -119.88642 37.49470 -119.19640 38.18515Next, we can retrieve observations within the bounding box of the
park. By default, the get_inat_obs() will return the most
recent 100 observations:
## Retrieve the first 100 iNaturalist observations within the bounding box.
## Note we have to rearrange the coordinates of the bounding box a little bit to
## give get_inat_obs() what it expects
yose_inat_df <- get_inat_obs(bounds = yose_bnd_bb[c(2,1,4,3)], year = 2022)Inspect the results:
dim(yose_inat_df)[1] 100 37head(yose_inat_df)In order to plot these observations, let’s first convert the data frame into a sf object:
yose_inat_sf <- yose_inat_df %>%
select(longitude, latitude, datetime, common_name, scientific_name, user_login) %>%
st_as_sf(coords=c("longitude", "latitude"), crs=4326)
yose_inat_sfSimple feature collection with 100 features and 4 fields
Geometry type: POINT
Dimension: XY
Bounding box: xmin: -119.8834 ymin: 37.50313 xmax: -119.1968 ymax: 38.1744
Geodetic CRS: WGS 84
First 10 features:
datetime common_name scientific_name
1 2022-04-14 16:46:01 -0700 Pacific Dogwood Cornus nuttallii
2 2022-06-18 19:54:14 -0700 Steller's Jay Cyanocitta stelleri
3 2022-05-29 19:52:44 -0700 flowering plants Angiospermae
4 2022-06-25 12:54:00 -0700 Northern Thick-billed Fox Sparrow Passerella iliaca megarhyncha
5 2022-06-25 22:01:00 -0700 Gray-crowned Rosy-Finch Leucosticte tephrocotis
6 2022-07-23 08:27:08 -0700 sulfur buckwheat Eriogonum umbellatum
7 2022-06-25 20:06:00 -0700 Yellow-bellied Marmot Marmota flaviventris
8 2022-08-28 11:29:00 -0700 Brewer's cinquefoil Potentilla breweri
9 2022-08-28 11:34:00 -0700 Lemmon's Indian Paintbrush Castilleja lemmonii
10 2022-08-28 10:58:00 -0700 Greater Fritillaries Argynnis
user_login geometry
1 frank16962 POINT (-119.5572 37.7348)
2 hueyl POINT (-119.6005 37.74141)
3 mmnk1997 POINT (-119.5804 37.7018)
4 cameronjohnson2 POINT (-119.5383 37.8651)
5 cameronjohnson2 POINT (-119.6235 37.92146)
6 owen_hill10 POINT (-119.3716 37.87855)
7 cameronjohnson2 POINT (-119.4805 37.86814)
8 strixoccidentalis POINT (-119.2531 37.91316)
9 strixoccidentalis POINT (-119.253 37.9132)
10 strixoccidentalis POINT (-119.2525 37.9137)tmap_mode("plot")tmap mode set to plottingtm_shape(yose_bnd_ll) +
tm_borders(col = "red", lwd = 2) +
tm_shape(yose_inat_sf) +
tm_symbols()Next we’ll a taxon to our query. Yosemite has some endemic toads. We can tell iNaturalist we only only want certain species using the optional taxon_name argument. Here we’ll set it to Bufonidae (the toad family).
yose_toads_df <- get_inat_obs(bounds = yose_bnd_bb[c(2,1,4,3)],
taxon_name = "Bufonidae")
dim(yose_toads_df)[1] 100 37glimpse(yose_toads_df, width = 110)Rows: 100
Columns: 37
$ scientific_name <chr> "Anaxyrus", "Anaxyrus", "Anaxyrus canorus", "Bufonidae", "Anaxyrus"…
$ datetime <chr> "2023-08-08 11:31:25 -0700", "2023-08-08 11:29:18 -0700", "2023-07-…
$ description <chr> "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "",…
$ place_guess <chr> "Yosemite National Park, Groveland, CA, US", "Yosemite National Par…
$ latitude <dbl> 37.85569, 37.85571, 37.81554, 37.96541, 37.74634, 37.87759, 37.9358…
$ longitude <dbl> -119.2157, -119.2160, -119.3609, -119.2672, -119.5735, -119.3770, -…
$ tag_list <chr> "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "",…
$ common_name <chr> "North American Toads", "North American Toads", "Yosemite Toad", "T…
$ url <chr> "https://www.inaturalist.org/observations/178327407", "https://www.…
$ image_url <chr> "https://static.inaturalist.org/photos/310290293/medium.jpg", "http…
$ user_login <chr> "seancarson_", "seancarson_", "ljfilgas", "legolaws", "drjuliariley…
$ id <int> 178327407, 178326611, 178239691, 178191266, 178123790, 177561494, 1…
$ species_guess <chr> "", "", "", "True Toads", "", "True Toads", "Yosemite Toad", "Yosem…
$ iconic_taxon_name <chr> "Amphibia", "Amphibia", "Amphibia", "Amphibia", "Amphibia", "Amphib…
$ taxon_id <int> 64747, 64747, 64972, 21359, 64747, 21359, 64972, 64972, 64972, 6497…
$ num_identification_agreements <int> 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 2, 1…
$ num_identification_disagreements <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ observed_on_string <chr> "2023-08-08 11:31:25-07:00", "2023-08-08 11:29:18-07:00", "2023-07-…
$ observed_on <chr> "2023-08-08", "2023-08-08", "2023-07-31", "2023-08-12", "2023-08-12…
$ time_observed_at <chr> "2023-08-08 18:31:25 UTC", "2023-08-08 18:29:18 UTC", "2023-07-31 2…
$ time_zone <chr> "Pacific Time (US & Canada)", "Pacific Time (US & Canada)", "Pacifi…
$ positional_accuracy <int> 9, 7, 7, 8, 24, 188, NA, 4, NA, NA, 9, 5262, NA, 23, 25028, 43, 4, …
$ public_positional_accuracy <int> 9, 7, 28329, 8, 24, 188, 28329, 28329, 28329, 28329, 28329, 5262, N…
$ geoprivacy <chr> "", "", "", "", "", "", "", "", "", "", "", "", "", "", "obscured",…
$ taxon_geoprivacy <chr> "", "", "obscured", "", "", "", "obscured", "obscured", "obscured",…
$ coordinates_obscured <chr> "false", "false", "true", "false", "false", "false", "true", "true"…
$ positioning_method <chr> "", "", "", "", "", "gps", "", "", "", "", "", "", "", "", "", "", …
$ positioning_device <chr> "", "", "", "", "", "gps", "", "", "", "", "", "", "", "", "", "", …
$ user_id <int> 923276, 923276, 2301182, 223936, 2048508, 2954954, 10326, 2383135, …
$ user_name <chr> "Sean Carson", "Sean Carson", "", "Eric Laws", "Dr. Julia Riley", "…
$ created_at <chr> "2023-08-14 06:55:28 UTC", "2023-08-14 06:42:45 UTC", "2023-08-13 1…
$ updated_at <chr> "2023-08-14 06:55:37 UTC", "2023-08-14 06:55:25 UTC", "2023-08-13 1…
$ quality_grade <chr> "needs_id", "needs_id", "needs_id", "needs_id", "casual", "needs_id…
$ license <chr> "", "", "CC-BY-NC", "CC-BY-NC", "", "", "CC-BY-NC-ND", "", "CC-BY-N…
$ sound_url <chr> "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "",…
$ oauth_application_id <int> 3, 3, 3, NA, 3, 2, NA, 3, NA, NA, 3, 3, 2, 3, NA, 3, 3, 3, 2, NA, 3…
$ captive_cultivated <chr> "false", "false", "false", "false", "false", "false", "false", "fal…Before we can plot it, we’ll convert the toads layer to a sf object. At the same time, we’ll reduce the number of columns to just those we want to include on the map.
yose_toads_sf <- yose_toads_df %>%
select(longitude, latitude, datetime, common_name, scientific_name, image_url, user_login) %>%
st_as_sf(coords=c("longitude", "latitude"), crs=4326)
yose_toads_sfSimple feature collection with 100 features and 5 fields
Geometry type: POINT
Dimension: XY
Bounding box: xmin: -119.8798 ymin: 37.49542 xmax: -119.2021 ymax: 38.11162
Geodetic CRS: WGS 84
First 10 features:
datetime common_name scientific_name
1 2023-08-08 11:31:25 -0700 North American Toads Anaxyrus
2 2023-08-08 11:29:18 -0700 North American Toads Anaxyrus
3 2023-07-31 16:20:32 -0700 Yosemite Toad Anaxyrus canorus
4 2023-08-12 15:39:00 -0700 True Toads Bufonidae
5 2023-08-12 21:18:05 -0700 North American Toads Anaxyrus
6 2023-08-04 13:55:47 -0700 True Toads Bufonidae
7 2023-07-31 09:17:00 -0700 Yosemite Toad Anaxyrus canorus
8 2023-08-04 13:24:09 -0700 Yosemite Toad Anaxyrus canorus
9 2023-07-31 07:37:00 -0700 Yosemite Toad Anaxyrus canorus
10 2023-07-31 07:42:00 -0700 Yosemite Toad Anaxyrus canorus
image_url user_login
1 https://static.inaturalist.org/photos/310290293/medium.jpg seancarson_
2 https://static.inaturalist.org/photos/310290266/medium.jpg seancarson_
3 https://inaturalist-open-data.s3.amazonaws.com/photos/310116072/medium.jpg ljfilgas
4 https://inaturalist-open-data.s3.amazonaws.com/photos/310014015/medium.jpeg legolaws
5 drjuliariley
6 https://static.inaturalist.org/photos/308836043/medium.jpeg jessicafriedman1
7 https://inaturalist-open-data.s3.amazonaws.com/photos/307573855/medium.jpeg natureali
8 https://static.inaturalist.org/photos/307216487/medium.jpg nyasa
9 https://inaturalist-open-data.s3.amazonaws.com/photos/306369732/medium.jpeg twillrichardson
10 https://inaturalist-open-data.s3.amazonaws.com/photos/306369714/medium.jpeg twillrichardson
geometry
1 POINT (-119.2157 37.85569)
2 POINT (-119.216 37.85571)
3 POINT (-119.3609 37.81554)
4 POINT (-119.2672 37.96541)
5 POINT (-119.5735 37.74634)
6 POINT (-119.377 37.87759)
7 POINT (-119.3918 37.93588)
8 POINT (-119.2021 37.88905)
9 POINT (-119.2878 37.9705)
10 POINT (-119.3019 37.96713)We’ll make the interactive map with leaflet, instead of tmap, because leaflet gives us more control over the popup windows.
The first step is to add a column to the sf object that contains the HTML code that will appear in the popup windows. We’ll add this column using mutate, and the save the result as a new sf object:
## Add a column containing HTML that will appear in the popup windows
yose_toads_popup_sf <- yose_toads_sf %>%
mutate(popup_html = paste0("<p><b>", common_name, "</b><br/>",
"<i>", scientific_name, "</i></p>",
"<p>Observed: ", datetime, "<br/>",
"User: ", user_login, "</p>",
"<p><img src='", image_url, "' style='width:100%;'/></p>")
)This is what the HTML code looks like for the first feature:
yose_toads_popup_sf$popup_html[1][1] "<p><b>North American Toads</b><br/><i>Anaxyrus</i></p><p>Observed: 2023-08-08 11:31:25 -0700<br/>User: seancarson_</p><p><img src='https://static.inaturalist.org/photos/310290293/medium.jpg' style='width:100%;'/></p>"Make the map
leaflet(yose_toads_popup_sf) %>%
addTiles() %>%
addCircleMarkers(popup = ~popup_html, radius = 5)Search for iNaturalist observations for your favorite Yosemite animal
or plant by passing a Family, Genus or Species to
get_inat_obs(). You could specify for example
Ursidae (bears), Sequoiadendron (Sequoia), or
Lilium (lilies). Answer
taxon <- c("Ursidae", "Sequoiadendron", "Lilium")[1]
yose_taxon_sf <- get_inat_obs(bounds = yose_bnd_bb[c(2,1,4,3)],
taxon_name = taxon) %>%
select(longitude, latitude, datetime, common_name, scientific_name,
image_url, user_login) %>%
st_as_sf(coords=c("longitude", "latitude"), crs=4326)
yose_taxon_sf <- yose_taxon_sf %>%
mutate(popup_html = paste0("<p><b>", common_name, "</b><br/>",
"<i>", scientific_name, "</i></p>",
"<p>Observed: ", datetime, "<br/>",
"User: ", user_login, "</p>",
"<p><img src='", image_url, "' style='width:100%;'/></p>"))
leaflet(yose_taxon_sf) %>%
addTiles() %>%
addCircleMarkers(popup = ~popup_html, radius = 5)Congratulations, you’ve completed the Notebook!
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