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Add selected species that were analysed for ABV. Add red list data Fl…
…anders.
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EmmaCartuyvels1
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--- | ||
title: '"Trend modelling"' | ||
author: "Emma Cartuyvels, Ward Langeraert, Toon Van Daele" | ||
date: "2024-10-29" | ||
output: html_document | ||
--- | ||
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```{r setup, include=FALSE} | ||
library(tidyverse) | ||
knitr::opts_chunk$set(echo = TRUE) | ||
``` | ||
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```{r data, cache=TRUE} | ||
birdcubeflanders_year_sf <- read_sf(here::here("data", "interim", | ||
"birdcubeflanders_year.gpkg")) | ||
abv_data_total_sf <- read_sf(here::here("data", "interim", | ||
"abv_data_total.gpkg")) | ||
``` | ||
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```{r transform abv} | ||
abv_data_total <- abv_data_total_sf |> | ||
st_drop_geometry() |> | ||
mutate(cyclus = case_when( | ||
year >= 2007 & year <= 2009 ~ 1, | ||
year >= 2010 & year <= 2012 ~ 2, | ||
year >= 2013 & year <= 2015 ~ 3, | ||
year >= 2016 & year <= 2018 ~ 4, | ||
year >= 2019 & year <= 2021 ~ 5, | ||
year >= 2022 & year <= 2024 ~ 6 | ||
)) |> | ||
mutate(species = case_when( | ||
species == "Parus montanus" ~ "Poecile montanus", | ||
species == "Dendrocopus major" ~ "Dendrocopos major", | ||
species == "Saxicola torquatus" ~ "Saxicola rubicola", | ||
TRUE ~ species | ||
)) |> | ||
group_by(species) |> | ||
mutate(n_obs = n()) |> | ||
ungroup() |> | ||
mutate(category = cut(n_obs, | ||
breaks = c(0, 10, 100, 1000, 10000, +Inf), | ||
labels = c("Very rare", "Rare", "Common", | ||
"Very common", "Extremely common"), | ||
right = FALSE)) | ||
birdcubeflanders_year <- birdcubeflanders_year_sf |> | ||
st_drop_geometry() |> | ||
mutate(cyclus = case_when( | ||
year >= 2007 & year <= 2009 ~ 1, | ||
year >= 2010 & year <= 2012 ~ 2, | ||
year >= 2013 & year <= 2015 ~ 3, | ||
year >= 2016 & year <= 2018 ~ 4, | ||
year >= 2019 & year <= 2021 ~ 5, | ||
year >= 2022 & year <= 2024 ~ 6 | ||
)) | ||
abv_data_total_tf <- abv_data_total |> | ||
group_by(species, year, TAG, category) |> | ||
summarise(n = sum(individualCount)) |> | ||
ungroup() | ||
``` | ||
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```{r} | ||
abv_ana_birds <- c( | ||
"Cetti's zanger", "Putter", "Kleine mantelmeeuw", "Roek", "Kuifeend", | ||
"Halsbandparkiet", "Aalscholver", "Kauw", "Buizerd", "Nijlgans", | ||
"Roodborsttapuit", "Boomklever", "Meerkoet", "Zwarte roodstaart", | ||
"Grote bonte specht", "Roodborst", "Krakeend", "Boomleeuwerik", | ||
"Bonte vliegenvanger", "Grauwe gans", "Torenvalk", "Zwartkop", | ||
"Witte kwikstaart", "Boomkruiper", "Grasmus", "Pimpelmees", "Vink", | ||
"Boerenzwaluw", "Tjiftjaf", "Zwarte kraai", "Houtduif", "Kleine karekiet", | ||
"Fazant", "Gaai", "Groene specht", "Ekster", "Koolmees", "Gele kwikstaart", | ||
"Groenling", "Holenduif", "Winterkoning", "Scholekster", "Koekoek", | ||
"Heggenmus", "Spreeuw", "Turkse tortel", "Veldleeuwerik", "Geelgors", | ||
"Goudhaan", "Kuifmees", "Zilvermeeuw", "Matkop", "Huismus", "Wilde eend", | ||
"Waterhoen", "Zanglijster", "Merel", "Tuinfluiter", "Zwarte mees", "Patrijs", | ||
"Graspieper", "Fitis", "Stadsduif", "Wielewaal", "Grutto", "Kievit", | ||
"Grote lijster", "Ringmus", "Sprinkhaanzanger", "Kokmeeuw", "Sperwer", | ||
"Bruine kiekendief", "Fuut", "Gekraagde roodstaart", "Bergeend", "Kneu", | ||
"Rietzanger", "Blauwe reiger", "Wulp", "Blauwborst", "Zwarte specht", | ||
"Boompieper", "Rietgors", "Canadese gans", "Spotvogel", "Bosrietzanger", | ||
"Knobbelzwaan", "Havik", "Glanskop", "Middelste Bonte Specht", "Tafeleend", | ||
"Gierzwaluw", "Nachtegaal", "Huiszwaluw", "Staartmees", "Dodaars" | ||
) | ||
abv_ana_birds <- data.frame(abv_ana_birds) |> | ||
left_join(abv_data_total |> distinct(vernacularName, species), | ||
by = join_by(abv_ana_birds == vernacularName)) | ||
``` | ||
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```{r} | ||
data_path <- here::here("data", "raw") | ||
red_list_fl1 <- read_delim(file.path(data_path, | ||
"dwca-rl-flanders-validated-checklist-v1.7", | ||
"distribution.txt"), | ||
delim = "\t", | ||
show_col_types = FALSE) | ||
red_list_fl2 <- read_delim(file.path(data_path, | ||
"dwca-rl-flanders-validated-checklist-v1.7", | ||
"taxon.txt"), | ||
delim = "\t", | ||
show_col_types = FALSE) | ||
``` | ||
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