I have this script to download observational data of a species from GBIF.org in R. Afterwards, the data is plotted on a map of Europe so make a map of the species distribution.
# PACKAGES
library(sf)
library(rgbif)
library(dismo)
library(tidyverse)
library(eurostat)
library(leaflet)
library(sf)
library(scales)
library(cowplot)
library(ggthemes)
library(ggplot2)
# GBIF EXAMPLE
# Get data from GBIF
data <- gbif("Psilocybe", "semilanceata", geo = TRUE)
# Filter out rows with missing coordinates
data_filtered <- data[complete.cases(data$lon, data$lat), ]
# Create a spatial dataframe
data_sf <- st_as_sf(data_filtered, coords = c("lon", "lat"), crs = 4326)
# MAP
# Get map data
get_eurostat_geospatial(resolution = 10,
nuts_level = 0,
year = 2016)
SHP_0 <- get_eurostat_geospatial(resolution = 10,
nuts_level = 0,
year = 2016)
# PLOT OBSERVATIONS + MAP
# Simple
species_plot <-ggplot() +
geom_sf() +
geom_sf(data = SHP_0, color = 'black', fill = 'grey90',linewidth = 0.20) +
scale_x_continuous(limits = c(-10, 30)) +
scale_y_continuous(limits = c(35, 70)) +
geom_sf(data = data_sf, color = "cornflowerblue", size = 1.2, alpha = 0.25) +
theme_void()
# Save the ggplot as a .jpg file with the species name
species_name <- "Psilocybe_semilanceata"
ggsave(paste0(species_name, ".jpg"), plot = species_plot, width = 10, height = 8, units = "in", dpi = 300)
I have a complete dataset with a few hundred species which I want to make a distribution map for. So, I loaded the dataset with the Latin species name:
> str(bird_names)
chr [1:280] "Prunella modularis" "Myiopsitta monachus" ...
> head(bird_names)
[1] "Prunella modularis" "Myiopsitta monachus" "Pyrrhura perlata"
[4] "Tyto alba" "Panurus biarmicus" "Merops apiaster"
Therefore I rewrote the first script with a for-loop to download all the species data from GBIF.org and plot it:
library(sf)
library(rgbif)
library(dismo)
library(tidyverse)
library(eurostat)
library(leaflet)
library(sf)
library(scales)
library(cowplot)
library(ggthemes)
library(ggplot2)
# Create a directory for storing bird maps
dir.create("BIRD_MAPS", showWarnings = FALSE)
# Your existing packages and GBIF example...
# Loop through each bird species
for (species in bird_names) {
# Split the species name into genus and species
species_parts <- strsplit(species, " ")[[1]]
genus <- species_parts[1]
species_name <- species_parts[2]
# Get data from GBIF for the current species
data <- gbif(genus, species_name, geo = TRUE)
# Filter out rows with missing coordinates
data_filtered <- data[complete.cases(data$lon, data$lat), ]
# Create a spatial dataframe
data_sf <- st_as_sf(data_filtered, coords = c("lon", "lat"), crs = 4326)
# Get map data
SHP_0 <- get_eurostat_geospatial(resolution = 10, nuts_level = 0, year = 2016)
# Plot observations + map
species_plot <- ggplot() +
geom_sf() +
geom_sf(data = SHP_0, color = 'black', fill = 'grey90', linewidth = 0.20) +
scale_x_continuous(limits = c(-10, 30)) +
scale_y_continuous(limits = c(35, 70)) +
geom_sf(data = data_sf, color = "cornflowerblue", size = 1.2, alpha = 0.25) +
theme_void()
# Save the ggplot as a .jpg file with the species name in BIRD_MAPS directory
ggsave(paste0("BIRD_MAPS/", gsub(" ", "_", species), ".jpg"), plot = species_plot, width = 10, height = 8, units = "in", dpi = 300)
}
However, I got this error:
2790578 records found
Error in gbif(genus, species_name, geo = TRUE) :
The number of records is larger than the maximum for download via this service (200,000)
Is it possible to overcome this? Do I get the error because the script wants to download all observations at once instead of all the observations of one species? I only want the observations of Europe so that could be a way to filter out some excess observations.
As
L Tyronementioned, you can use argbifpackage. Below my standard workflow example to get the GBIF occurencies for species (including synonyms). Feel free to use it as guide:occ_countfor them:rgbifuses GBIF API, therefore you have to create an account on GBIF.CoordinateCleanerpackage to clean up the data, like: