Created
October 16, 2025 13:04
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Occurrences of Passerines in South America, 3 most common genera
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# Passerines in South America | |
# Data read from GBIF occurrence download (SQL QUERY) | |
pas_sa <- | |
rgbif::occ_download_get("0028483-251009101135966") |> | |
rgbif::occ_download_import() |> | |
dplyr::filter(!is.na(month)) | |
# Identify the 3 most common genera ------------------------------------- | |
common_genera <- pas_sa |> | |
dplyr::group_by(genuskey) |> | |
dplyr::summarise(n = sum(`COUNT(*)`)) |> | |
dplyr::slice_max(order_by = n, n = 3) |> | |
dplyr::mutate(genus = purrr::map_chr( | |
genuskey, | |
\(genuskey) { | |
rgbif::name_usage(genuskey)$data$canonicalName | |
}, | |
.progress = TRUE | |
)) |> | |
dplyr::select(-n) | |
# Add labels to data | |
pas_common <- | |
pas_sa |> | |
dplyr::mutate( | |
month_label = | |
purrr::map_chr(month, ~ as.character(lubridate::month(.x, label = TRUE, locale = "en_US.UTF-8"))) | |
) |> | |
dplyr::right_join(common_genera, by = dplyr::join_by("genuskey")) | |
# labels for species | |
species_labels <- pas_common |> | |
dplyr::distinct(specieskey) |> | |
dplyr::mutate(species = purrr::map_chr( | |
specieskey, | |
\(specieskey) { | |
rgbif::name_usage(specieskey)$data$canonicalName | |
}, | |
.progress = TRUE | |
)) | |
pas_common <- pas_common |> | |
dplyr::left_join(species_labels, by = dplyr::join_by("specieskey")) | |
# Plot the 3 most common genera ------------------------------------------- | |
library(ggplot2) | |
ggplot(pas_common) + | |
aes(x = month_label, y = `COUNT(*)`, fill = species, group = species) + | |
geom_col() + | |
scale_fill_hue(direction = 1) + | |
theme_minimal() + | |
facet_wrap(vars(genus)) + | |
labs( | |
title = "Monthly Observations of Common Passerine Species in South America", | |
subtitle = "3 most common genera", | |
x = "Month", | |
y = "Number of Observations", | |
fill = "Species" | |
) |
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