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Day 1 of 30DayMapChallenge: « Points » (previously).
Using data from GBIF to map species presence points.
# Register an account on https://www.gbif.org
# and save the credentials in ~/.Renviron :
# GBIF_USER="xxxx"
# GBIF_PWD="*****"
# GBIF_EMAIL="you@example.org"
library(rgbif)
library(tidyverse)
library(sf)
library(rnaturalearth)
library(ggtext)
library(glue)
# basemap
countries <- ne_countries(scale = "medium", returnclass = "sf")
# Get ID of the species
taxon <- name_backbone("Lynx lynx")
# Launch the query
occ_download(pred("taxonKey", taxon$usageKey),
format = "SIMPLE_CSV")
# Query status (your ID will differ)
occ_download_wait("0034730-231002084531237")
<<gbif download metadata>> Status: SUCCEEDED DOI: 10.15468/dl.jfaebj Format: SIMPLE_CSV Download key: 0034730-231002084531237 Created: 2023-11-01T17:52:20.752+00:00 Modified: 2023-11-01T17:54:02.517+00:00 Download link: https://api.gbif.org/v1/occurrence/download/request/0034730-231002084531237.zip Total records: 77187
# Get results
lynx <- occ_download_get("0034730-231002084531237") |>
occ_download_import()
glimpse(lynx)
Rows: 77,187 Columns: 50 $ gbifID <int64> 991907429, 924537973, 924537972, 92… $ datasetKey <chr> "b7ec1bf8-819b-11e2-bad2-00145eb45e9a… $ occurrenceID <chr> "", "7408f0e4-f81d-11e6-ae10-70e2840f… $ kingdom <chr> "Animalia", "Animalia", "Animalia", "… $ phylum <chr> "Chordata", "Chordata", "Chordata", "… $ class <chr> "Mammalia", "Mammalia", "Mammalia", "… $ order <chr> "Carnivora", "Carnivora", "Carnivora"… $ family <chr> "Felidae", "Felidae", "Felidae", "Fel… $ genus <chr> "Lynx", "Lynx", "Lynx", "Lynx", "Lynx… $ species <chr> "Lynx lynx", "Lynx lynx", "Lynx lynx"… $ infraspecificEpithet <chr> "", "", "", "", "", "", "", "", "", "… $ taxonRank <chr> "SPECIES", "SPECIES", "SPECIES", "SPE… $ scientificName <chr> "Lynx lynx (Linnaeus, 1758)", "Lynx l… $ verbatimScientificName <chr> "Lynx lynx Linnaeus, 1758", "Lynx lyn… $ verbatimScientificNameAuthorship <chr> "", "", "", "", "", "", "", "", "", "… $ countryCode <chr> "DE", "", "", "SE", "DE", "CA", "DE",… $ locality <chr> "Tierpark Berlin", "", "", "Vansbro K… $ stateProvince <chr> "", "", "", "", "", "", "", "", "", "… $ occurrenceStatus <chr> "PRESENT", "PRESENT", "PRESENT", "PRE… $ individualCount <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, N… $ publishingOrgKey <chr> "10980920-6dad-11da-ad13-b8a03c50a862… $ decimalLatitude <dbl> NA, NA, NA, 60.52402, 51.63549, 50.80… $ decimalLongitude <dbl> NA, NA, NA, 14.179573, 10.787888, -10… $ coordinateUncertaintyInMeters <dbl> NA, NA, NA, 250, 250, 250, 250, 250, … $ coordinatePrecision <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N… $ elevation <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N… $ elevationAccuracy <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N… $ depth <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N… $ depthAccuracy <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N… $ eventDate <dttm> 1962-01-13 15:00:00, NA, NA, 2003-07… $ day <int> 13, NA, NA, 24, 15, 28, 6, 6, 28, 6, … $ month <int> 1, NA, NA, 7, 3, 8, 5, 8, 5, 8, 1, 9,… $ year <int> 1962, NA, NA, 2003, 2012, 2011, 2011,… $ taxonKey <int> 2435240, 2435240, 2435240, 2435240, 2… $ speciesKey <int> 2435240, 2435240, 2435240, 2435240, 2… $ basisOfRecord <chr> "OBSERVATION", "PRESERVED_SPECIMEN", … $ institutionCode <chr> "MfN", "KPM", "KPM", "naturgucker", "… $ collectionCode <chr> "TSA", "NFM", "NFM", "naturgucker", "… $ catalogNumber <chr> "TSA:Lynx_lynx_S_674_2_1", "KPM-NFM00… $ recordNumber <chr> "", "", "", "", "", "", "", "", "", "… $ identifiedBy <chr> "", "", "", "", "", "", "", "", "", "… $ dateIdentified <dttm> NA, NA, NA, NA, NA, NA, NA, NA, NA, … $ license <chr> "CC_BY_4_0", "CC_BY_4_0", "CC_BY_4_0"… $ rightsHolder <chr> "", "", "", "", "", "", "", "", "", "… $ recordedBy <chr> "Tembrock, Günter", "", "", "34172526… $ typeStatus <chr> "", "", "", "", "", "", "", "", "", "… $ establishmentMeans <chr> "", "", "", "", "", "", "", "", "", "… $ lastInterpreted <dttm> 2023-08-26 10:10:45, 2023-10-14 04:4… $ mediaType <chr> "Sound", "", "", "", "", "", "", "", … $ issue <chr> "CONTINENT_DERIVED_FROM_COUNTRY", "IN…
# Some cleaning (valid coords, presence, on land)
lynx_geo <- lynx |>
drop_na(decimalLongitude, decimalLatitude) |>
filter(occurrenceStatus == "PRESENT",
!near(decimalLongitude, 0) & !near(decimalLatitude, 0)) |>
st_as_sf(coords = c("decimalLongitude", "decimalLatitude"), crs = "EPSG:4326") |>
st_join(st_make_valid(countries), left = FALSE)
# Map
ggplot(lynx_geo) +
geom_sf(data = countries) +
geom_sf(color = "red", size = 0.1, alpha = 0.05) +
coord_sf(xlim = c(2800000, 7000000), ylim = c(2000000, 5300000), crs = "EPSG:3035") +
labs(title = "_Lynx lynx_ occurrence",
subtitle = glue("Europe, {min(lynx_geo$year, na.rm = TRUE)} - {max(lynx_geo$year, na.rm = TRUE)}"),
caption = glue("GBIF occurrence download https://doi.org/10.15468/dl.jfaebj
Basemap: Natural Earth
https://r.iresmi.net/")) +
theme(plot.caption = element_text(size = 7),
plot.title = element_markdown())
Well, I guess the contributions are unequal between countries (Sweden?) and some cleaning should be done (sightings in North Atlantic and at Null Island!).
There is a lot of overplotting; we should do some smoothing…
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