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required_packages <- c( |
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"httr", "jsonlite", "tidyverse", "glue", "lubridate", |
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"wesanderson", "viridis", "hexbin", "shinycssloaders", |
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"DT", "maps", "mapdata", "leaflet", "leaflet.extras", |
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"shinythemes", "shiny", "arrow" |
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) |
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installed_packages <- rownames(installed.packages()) |
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for (pkg in required_packages) { |
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if (!pkg %in% installed_packages) install.packages(pkg, dependencies = TRUE) |
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} |
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library(httr) |
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library(jsonlite) |
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library(tidyverse) |
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library(glue) |
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library(lubridate) |
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library(wesanderson) |
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library(viridis) |
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library(hexbin) |
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library(shinycssloaders) |
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library(DT) |
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library(maps) |
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library(mapdata) |
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library(leaflet) |
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library(leaflet.extras) |
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library(shinythemes) |
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library(shiny) |
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library(arrow) |
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parquet_path <- "https://huggingface.co/datasets/diegoellissoto/iNaturalist_mortality_records_12Apr2025/resolve/main/inat_all_Apr122025.parquet" |
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make_daily_plot <- function(df, start_date, end_date) { |
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if (!"observed_on" %in% names(df)) return(ggplot() + theme_void() + labs(title = "No date info")) |
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if (nrow(df) == 0) return(ggplot() + theme_void() + labs(title = "No data")) |
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df <- df %>% |
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|
mutate(obs_date = as.Date(observed_on), |
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Window = format(obs_date, "%Y")) %>% |
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|
filter(!is.na(obs_date)) |
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|
counts_by_day <- df %>% |
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|
group_by(Window, obs_date) %>% |
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|
summarise(n = n_distinct(id), .groups = "drop") |
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y_max_value <- max(counts_by_day$n, na.rm = TRUE) |
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|
ggplot(counts_by_day, aes(x = obs_date, y = n, color = Window)) + |
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|
geom_line(size = 1.2) + |
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|
geom_point(size = 2) + |
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|
scale_x_date(date_labels = "%b %d", date_breaks = "1 month") + |
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|
scale_y_continuous(limits = c(0, y_max_value)) + |
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labs( |
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title = glue("Daily 'Dead' Observations ({start_date} to {end_date})"), |
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|
x = "Date", |
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|
y = "Number of Observations", |
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|
color = "Year" |
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|
) + |
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|
theme_minimal(base_size = 14) + |
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|
theme(axis.text.x = element_text(angle = 45, hjust = 1)) |
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} |
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make_top_species_plot <- function(df) { |
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|
if (!"scientific_name" %in% names(df)) return(ggplot() + theme_void() + labs(title = "No species info")) |
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|
if (nrow(df) == 0) return(ggplot() + theme_void() + labs(title = "No data")) |
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|
df <- df %>% |
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|
mutate(obs_date = as.Date(observed_on), |
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|
Window = format(obs_date, "%Y")) |
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|
species_counts <- df %>% |
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|
filter(!is.na(scientific_name)) %>% |
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|
group_by(Window, scientific_name) %>% |
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|
summarise(dead_count = n(), .groups = "drop") |
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|
top_species_overall <- species_counts %>% |
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|
group_by(scientific_name) %>% |
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|
summarise(total_dead = sum(dead_count)) %>% |
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|
arrange(desc(total_dead)) %>% |
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|
slice_head(n = 20) |
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|
species_top20 <- species_counts %>% |
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|
filter(scientific_name %in% top_species_overall$scientific_name) |
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|
ggplot(species_top20, aes( |
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|
x = reorder(scientific_name, -dead_count), |
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|
y = dead_count, |
|
|
fill= Window |
|
|
)) + |
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|
geom_col(position = position_dodge(width = 0.7)) + |
|
|
coord_flip() + |
|
|
labs( |
|
|
title = "Top 20 Species with 'Dead' Observations", |
|
|
x = "Species", |
|
|
y = "Number of Dead Observations", |
|
|
fill = "Year" |
|
|
) + |
|
|
theme_minimal(base_size = 14) |
|
|
} |
|
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|
|
|
make_hexbin_map <- function(df, start_date, end_date) { |
|
|
if (!("latitude" %in% names(df) && "longitude" %in% names(df))) { |
|
|
return(ggplot() + labs(title = "No spatial data available for map") + theme_void()) |
|
|
} |
|
|
df <- df %>% filter(!is.na(latitude) & !is.na(longitude)) |
|
|
if (nrow(df) == 0) { |
|
|
return(ggplot() + labs(title = "No spatial data available for map") + theme_void()) |
|
|
} |
|
|
x_limits <- range(df$longitude, na.rm = TRUE) |
|
|
y_limits <- range(df$latitude, na.rm = TRUE) |
|
|
ggplot() + |
|
|
borders("world", fill = "gray80", colour = "white") + |
|
|
stat_bin_hex( |
|
|
data = df, |
|
|
aes(x = longitude, y = latitude), |
|
|
bins = 500, |
|
|
color = "black", |
|
|
alpha = 0.8 |
|
|
) + |
|
|
|
|
|
scale_fill_viridis_c(option = "magma", name = "Obs. Count", trans="sqrt") + |
|
|
coord_quickmap(xlim = x_limits, ylim = y_limits, expand = TRUE) + |
|
|
labs( |
|
|
title = glue("'Dead' Wildlife Hexbin Map ({start_date} to {end_date})"), |
|
|
x = "Longitude", |
|
|
y = "Latitude" |
|
|
) + |
|
|
theme_classic(base_size = 14) + |
|
|
theme( |
|
|
axis.text = element_text(face = "bold", size = 14, colour = "black"), |
|
|
axis.title = element_text(face = "bold", size = 16, colour = "black") |
|
|
) |
|
|
} |
|
|
|
|
|
get_high_mortality_days <- function(df) { |
|
|
if (!"observed_on" %in% names(df)) return(NULL) |
|
|
df <- df %>% mutate(obs_date = as.Date(observed_on)) |
|
|
counts_by_day <- df %>% |
|
|
group_by(obs_date) %>% |
|
|
summarise(n = n_distinct(id), .groups = "drop") |
|
|
if (nrow(counts_by_day) == 0) return(NULL) |
|
|
daily_quantile <- quantile(counts_by_day$n, probs = 0.90, na.rm = TRUE) |
|
|
high_days <- counts_by_day %>% filter(n >= daily_quantile) %>% pull(obs_date) |
|
|
list(days = high_days, quant = daily_quantile) |
|
|
} |
|
|
|
|
|
|
|
|
fetch_dead_data_once <- function( |
|
|
swlat, swlng, nelat, nelng, |
|
|
start_date, end_date, |
|
|
iconic_taxa = NULL, taxon_name = NULL, |
|
|
per_page = 200, max_pages = 200, progress = NULL |
|
|
) { |
|
|
base_url <- "https://api.inaturalist.org/v1/observations" |
|
|
q_parts <- list( |
|
|
"term_id=17", "term_value_id=19", "verifiable=true", |
|
|
glue("d1={start_date}"), glue("d2={end_date}"), |
|
|
"order=desc", "order_by=created_at", glue("per_page={per_page}") |
|
|
) |
|
|
if (!is.null(iconic_taxa) && iconic_taxa != "") q_parts <- c(q_parts, glue("iconic_taxa={iconic_taxa}")) |
|
|
if (!is.null(taxon_name) && taxon_name != "") q_parts <- c(q_parts, glue("taxon_name={URLencode(taxon_name)}")) |
|
|
query_params <- paste(q_parts, collapse = "&") |
|
|
loc_part <- glue("&nelat={nelat}&nelng={nelng}&swlat={swlat}&swlng={swlng}") |
|
|
observations_list <- list() |
|
|
current_page <- 1 |
|
|
while (current_page <= max_pages) { |
|
|
if (!is.null(progress)) progress$set(detail = glue("API page {current_page}"), value = NULL) |
|
|
query_url <- paste0(base_url, "?", query_params, "&page=", current_page, loc_part) |
|
|
resp <- GET(query_url) |
|
|
if (http_error(resp)) { |
|
|
warning("HTTP error on page ", current_page, ": ", status_code(resp)) |
|
|
break |
|
|
} |
|
|
parsed <- content(resp, as = "text", encoding = "UTF-8") %>% |
|
|
fromJSON(flatten = TRUE) |
|
|
if (length(parsed$results) == 0) break |
|
|
obs_page_df <- as_tibble(parsed$results) |
|
|
observations_list[[current_page]] <- obs_page_df |
|
|
if (nrow(obs_page_df) < per_page) break |
|
|
current_page <- current_page + 1 |
|
|
Sys.sleep(1.4) |
|
|
} |
|
|
bind_rows(observations_list) |
|
|
} |
|
|
|
|
|
getDeadVertebrates_dateRange <- function( |
|
|
start_date, end_date, |
|
|
swlat, swlng, nelat, nelng, |
|
|
iconic_taxa = NULL, taxon_name = NULL, |
|
|
per_page = 500, max_pages = 500, |
|
|
.shiny_progress = NULL |
|
|
) { |
|
|
start_date <- as.Date(start_date) |
|
|
end_date <- as.Date(end_date) |
|
|
week_starts <- seq.Date(start_date, end_date, by = "1 week") |
|
|
all_weeks_list <- list() |
|
|
for (i in seq_along(week_starts)) { |
|
|
st <- week_starts[i] |
|
|
ed <- if (i < length(week_starts)) week_starts[i + 1] - 1 else end_date |
|
|
if (!is.null(.shiny_progress)) { |
|
|
.shiny_progress$set( |
|
|
value = (i-1)/length(week_starts), |
|
|
message = glue("Live Query: Fetching week {i} of {length(week_starts)}"), |
|
|
detail = glue("Dates: {st} to {ed}") |
|
|
) |
|
|
} |
|
|
df_week <- fetch_dead_data_once( |
|
|
swlat, swlng, nelat, nelng, |
|
|
start_date = st, end_date = ed, |
|
|
iconic_taxa = iconic_taxa, taxon_name = taxon_name, |
|
|
per_page = per_page, max_pages = max_pages, |
|
|
progress = .shiny_progress |
|
|
) |
|
|
all_weeks_list[[i]] <- df_week |
|
|
Sys.sleep(1.4) |
|
|
} |
|
|
merged_df_all <- bind_rows(all_weeks_list) |
|
|
|
|
|
if (!"created_at_details.date" %in% names(merged_df_all) || nrow(merged_df_all) == 0) { |
|
|
placeholder_plot <- function(title) { |
|
|
ggplot() + labs(title = title, x = NULL, y = NULL) + theme_void() |
|
|
} |
|
|
return(list( |
|
|
merged_df_all = merged_df_all, |
|
|
merged_df = merged_df_all, |
|
|
daily_plot = placeholder_plot("No 'Dead' Observations Found"), |
|
|
top_species_plot = placeholder_plot("No species data"), |
|
|
map_hotspots_gg = placeholder_plot("No data for map"), |
|
|
daily_90th_quant = NA |
|
|
)) |
|
|
} |
|
|
merged_df_all <- merged_df_all %>% |
|
|
mutate(obs_date = as.Date(observed_on), |
|
|
Window = format(obs_date, "%Y")) |
|
|
counts_by_day <- merged_df_all %>% |
|
|
group_by(Window, obs_date) %>% |
|
|
summarise(n = n_distinct(id), .groups = "drop") |
|
|
y_max_value <- max(counts_by_day$n, na.rm = TRUE) |
|
|
daily_plot <- ggplot(counts_by_day, aes(x = obs_date, y = n, color = Window)) + |
|
|
geom_line(size = 1.2) + |
|
|
geom_point(size = 2) + |
|
|
scale_x_date(date_labels = "%b %d", date_breaks = "1 month") + |
|
|
scale_y_continuous(limits = c(0, y_max_value)) + |
|
|
labs( |
|
|
title = glue("Daily 'Dead' Observations ({start_date} to {end_date})"), |
|
|
x = "Date", |
|
|
y = "Number of Observations", |
|
|
color = "Year" |
|
|
) + |
|
|
theme_minimal(base_size = 14) + |
|
|
theme(axis.text.x = element_text(angle = 45, hjust = 1)) |
|
|
if ("taxon.name" %in% names(merged_df_all)) { |
|
|
species_counts <- merged_df_all %>% |
|
|
filter(!is.na(taxon.name)) %>% |
|
|
group_by(Window, taxon.name) %>% |
|
|
summarise(dead_count = n(), .groups = "drop") |
|
|
top_species_overall <- species_counts %>% |
|
|
group_by(taxon.name) %>% |
|
|
summarise(total_dead = sum(dead_count)) %>% |
|
|
arrange(desc(total_dead)) %>% |
|
|
slice_head(n = 20) |
|
|
species_top20 <- species_counts %>% |
|
|
filter(taxon.name %in% top_species_overall$taxon.name) |
|
|
top_species_plot <- ggplot(species_top20, aes( |
|
|
x = reorder(taxon.name, -dead_count), |
|
|
y = dead_count, |
|
|
fill= Window |
|
|
)) + |
|
|
geom_col(position = position_dodge(width = 0.7)) + |
|
|
coord_flip() + |
|
|
labs( |
|
|
title = "Top 20 Species with 'Dead' Observations", |
|
|
x = "Species", |
|
|
y = "Number of Dead Observations", |
|
|
fill = "Year" |
|
|
) + |
|
|
theme_minimal(base_size = 14) |
|
|
} else { |
|
|
top_species_plot <- ggplot() + |
|
|
labs(title = "No 'taxon.name' column found", x = NULL, y = NULL) + |
|
|
theme_void() |
|
|
} |
|
|
daily_quantile <- quantile(counts_by_day$n, probs = 0.90, na.rm = TRUE) |
|
|
high_mortality_days <- counts_by_day %>% |
|
|
filter(n >= daily_quantile) %>% |
|
|
pull(obs_date) |
|
|
merged_high <- merged_df_all %>% |
|
|
filter(obs_date %in% high_mortality_days) |
|
|
if ("location" %in% names(merged_df_all)) { |
|
|
location_df_all <- merged_df_all %>% |
|
|
filter(!is.na(location) & location != "") %>% |
|
|
separate(location, into = c("lat_str", "lon_str"), sep = ",", remove = FALSE) %>% |
|
|
mutate(latitude = as.numeric(lat_str), longitude = as.numeric(lon_str)) |
|
|
if (nrow(location_df_all) == 0) { |
|
|
map_hotspots_gg <- ggplot() + |
|
|
labs(title = "No spatial data available for map") + |
|
|
theme_void() |
|
|
} else { |
|
|
x_limits <- range(location_df_all$longitude, na.rm = TRUE) |
|
|
y_limits <- range(location_df_all$latitude, na.rm = TRUE) |
|
|
map_hotspots_gg <- ggplot() + |
|
|
borders("world", fill = "gray80", colour = "white") + |
|
|
stat_bin_hex( |
|
|
data = location_df_all, |
|
|
aes(x = longitude, y = latitude), |
|
|
bins = 500, |
|
|
color = "black", |
|
|
alpha = 0.8 |
|
|
) + |
|
|
scale_fill_viridis_c(option = "plasma", name = "Observation Count") + |
|
|
coord_quickmap(xlim = x_limits, ylim = y_limits, expand = TRUE) + |
|
|
labs( |
|
|
title = glue("'Dead' Wildlife Hexbin Map ({start_date} to {end_date})"), |
|
|
x = "Longitude", |
|
|
y = "Latitude" |
|
|
) + |
|
|
theme_classic(base_size = 14) + |
|
|
theme( |
|
|
axis.text = element_text(face = "bold", size = 14, colour = "black"), |
|
|
axis.title = element_text(face = "bold", size = 16, colour = "black") |
|
|
) |
|
|
} |
|
|
} else { |
|
|
map_hotspots_gg <- ggplot() + |
|
|
labs(title = "No 'location' column for map") + |
|
|
theme_void() |
|
|
} |
|
|
return(list( |
|
|
merged_df_all = merged_df_all, |
|
|
merged_df = merged_high, |
|
|
daily_plot = daily_plot, |
|
|
top_species_plot = top_species_plot, |
|
|
map_hotspots_gg = map_hotspots_gg, |
|
|
daily_90th_quant = daily_quantile |
|
|
)) |
|
|
} |
|
|
|
|
|
ui <- fluidPage( |
|
|
theme = shinytheme("cosmo"), |
|
|
fluidRow( |
|
|
column(width = 2, tags$img(src = "www/all_logos.png", height = "400px")), |
|
|
column(width = 10, titlePanel("Dead Wildlife Observations from iNaturalist")) |
|
|
), |
|
|
hr(), |
|
|
sidebarLayout( |
|
|
sidebarPanel( |
|
|
tabsetPanel(id = "sidebar_tabs", |
|
|
tabPanel("Query", |
|
|
br(), |
|
|
radioButtons( |
|
|
"data_source", "Data Source:", |
|
|
choices = c("Download Live from iNaturalist" = "live", "Archived Parquet File" = "archived"), |
|
|
selected = "live" |
|
|
), |
|
|
tags$div( |
|
|
style="margin-bottom:8px;", |
|
|
textInput("region_search", "Find place (type and click Search)", value = "", placeholder = "e.g. California, Uruguay, Yellowstone"), |
|
|
actionButton("region_search_btn", "Search", icon=icon("search")) |
|
|
), |
|
|
tags$div( |
|
|
style = "margin-bottom:10px;", |
|
|
leafletOutput("select_map", height = "340px"), |
|
|
actionButton("clear_bbox", "Clear Bounding Box", icon = icon("eraser")), |
|
|
helpText("Draw a rectangle or search for a place. Only one region (rectangle) is used at a time.") |
|
|
), |
|
|
verbatimTextOutput("bbox_coords"), |
|
|
dateRangeInput("date_range", "Select Date Range:", |
|
|
start = Sys.Date() - 365, |
|
|
end = Sys.Date(), |
|
|
min = "2010-01-01", |
|
|
max = Sys.Date()), |
|
|
radioButtons("query_type", "Query By:", |
|
|
choices = c("Taxon Class" = "iconic", "Exact Species Name" = "species")), |
|
|
conditionalPanel( |
|
|
condition = "input.query_type == 'iconic'", |
|
|
selectInput("iconic_taxon", "Select Taxon Class:", |
|
|
choices = c("Aves", "Mammalia", "Reptilia", "Amphibia", "Actinopterygii", "Mollusca", "Animalia"), |
|
|
selected = "Aves") |
|
|
), |
|
|
conditionalPanel( |
|
|
condition = "input.query_type == 'species'", |
|
|
textInput("species_name", "Enter exact species name (e.g. Puma concolor)", "") |
|
|
), |
|
|
actionButton("run_query", "Run Query", icon = icon("play")), |
|
|
hr(), |
|
|
downloadButton("downloadAll", "Download ALL Data CSV", icon = icon("download")) |
|
|
), |
|
|
tabPanel("About", |
|
|
tags$h3("iNaturalist, Dead Wildlife, and Participatory Science"), |
|
|
tags$p("iNaturalist is a global biodiversity platform powered by a vibrant community of naturalists, scientists, students, and citizens. Its open data and easy smartphone app allow anyone to record nature and contribute to science."), |
|
|
tags$h4("Why observe dead wildlife?"), |
|
|
tags$ul( |
|
|
tags$li("Track disease outbreaks and mass die-offs (e.g. avian influenza, amphibian disease)."), |
|
|
tags$li("Identify human-wildlife conflicts (e.g. roadkill, window strikes)."), |
|
|
tags$li("Detect range shifts and rare events."), |
|
|
tags$li("Monitor mortality of threatened or sensitive species.") |
|
|
), |
|
|
tags$p("Documenting dead wildlife—even if unpleasant—can save species by detecting threats early."), |
|
|
tags$h4("About this App"), |
|
|
tags$p("This app was created by Diego Ellis-Soto (UC Berkeley) and colleagues to empower rapid, open exploration of wildlife mortality patterns worldwide. It is open source and intended for research, conservation, and education."), |
|
|
tags$blockquote("Ellis-Soto D., Taylor L., Edson E., Schell C., Boettiger C., Johnson R. (2024). Global, near real-time ecological forecasting of mortality events through participatory science |
|
|
|
|
|
https://github.com/diego-ellis-soto/iNat_mortality_detector"), |
|
|
tags$h4("Technical Info"), |
|
|
tags$ul( |
|
|
tags$li("iNaturalist API v1 (Live Mode) and Parquet snapshot (Archive Mode).") |
|
|
), |
|
|
tags$h4("FAQ"), |
|
|
tags$dl( |
|
|
tags$dt("Can I use this data for research/publication?"), |
|
|
tags$dd("Yes! Always credit iNaturalist and respect original content licenses. See iNaturalist's Data Use Policy."), |
|
|
tags$dt("Why is the map sometimes empty?"), |
|
|
tags$dd("Some species/locations are obscured for privacy, or there may be no recent observations in your selected area and time."), |
|
|
tags$dt("Are locations accurate?"), |
|
|
tags$dd("Coordinate accuracy varies by observer and privacy settings."), |
|
|
tags$dt("Can I see private/sensitive records?"), |
|
|
tags$dd("No—privacy and ethical protection is strictly respected by the iNaturalist API and this app.") |
|
|
), |
|
|
tags$h4("Responsible Use"), |
|
|
tags$p("Never disturb wildlife for photos. Be cautious with sensitive data. Community-driven science works best when it's ethical and transparent."), |
|
|
tags$h4("Get Involved!"), |
|
|
tags$p("Join iNaturalist, share your own records, or help identify others' observations. Every data point helps conservation.") |
|
|
), |
|
|
tabPanel("How to Use", |
|
|
tags$h3("Quick Start Guide"), |
|
|
tags$ol( |
|
|
tags$li("Search for a place or draw a rectangle on the map (one region at a time)."), |
|
|
tags$li("Set your date range. For best speed, keep queries focused."), |
|
|
tags$li("Choose a taxon class or enter a species name."), |
|
|
tags$li("Pick 'Live' for the latest data (slower, but up-to-date) or 'Archive' for instant results (fixed snapshot)."), |
|
|
tags$li("Click Run Query. Visualizations and tables will update below!"), |
|
|
tags$li("Download the full results table as CSV for further analysis.") |
|
|
), |
|
|
tags$h4("Tips"), |
|
|
tags$ul( |
|
|
tags$li("Use Archive mode for large or exploratory queries—it is much faster."), |
|
|
tags$li("Live mode fetches week-by-week and may take minutes for big regions or long periods (a progress bar helps you track progress)."), |
|
|
tags$li("To reset your selected area, click 'Clear Bounding Box'.") |
|
|
), |
|
|
tags$h4("Contact & Support"), |
|
|
tags$p("For questions or feedback, visit our GitHub repository or email the authors.") |
|
|
) |
|
|
) |
|
|
), |
|
|
mainPanel( |
|
|
tabsetPanel( |
|
|
|
|
|
tabPanel("Daily Time Series", |
|
|
fluidRow( |
|
|
column(width = 8, withSpinner(plotOutput("dailyPlot"), type = 6)), |
|
|
column(width = 4, verbatimTextOutput("dailySummary")) |
|
|
) |
|
|
), |
|
|
tabPanel("Top Species", withSpinner(plotOutput("speciesPlot"), type = 6)), |
|
|
tabPanel("Hexbin Map (All Data)", withSpinner(plotOutput("hotspotMap"), type = 6)), |
|
|
tabPanel("All Data Table", withSpinner(DT::dataTableOutput("dataTable"), type = 6)) |
|
|
) |
|
|
) |
|
|
) |
|
|
) |
|
|
|
|
|
server <- function(input, output, session) { |
|
|
rv <- reactiveValues(bbox = NULL) |
|
|
output$select_map <- renderLeaflet({ |
|
|
leaflet() %>% addTiles() %>% |
|
|
setView(lng = -95, lat = 40, zoom = 3) %>% |
|
|
addDrawToolbar( |
|
|
targetGroup = "drawn_bboxes", |
|
|
rectangleOptions = drawRectangleOptions(repeatMode = FALSE), |
|
|
polylineOptions = FALSE, circleOptions = FALSE, |
|
|
markerOptions = FALSE, circleMarkerOptions = FALSE, |
|
|
polygonOptions = FALSE, editOptions = editToolbarOptions() |
|
|
) |
|
|
}) |
|
|
observeEvent(input$select_map_draw_new_feature, { |
|
|
feat <- input$select_map_draw_new_feature |
|
|
if (!is.null(feat$geometry) && feat$geometry$type == "Polygon") { |
|
|
coords <- feat$geometry$coordinates[[1]] |
|
|
lngs <- vapply(coords, function(x) x[[1]], numeric(1)) |
|
|
lats <- vapply(coords, function(x) x[[2]], numeric(1)) |
|
|
rv$bbox <- c(min(lats), min(lngs), max(lats), max(lngs)) |
|
|
} |
|
|
}) |
|
|
observeEvent(input$select_map_draw_deleted_features, { rv$bbox <- NULL }) |
|
|
observeEvent(input$select_map_draw_edited_features, { |
|
|
if (!is.null(input$select_map_draw_all_features)) { |
|
|
feats <- input$select_map_draw_all_features$features |
|
|
if (length(feats) > 0) { |
|
|
feat <- feats[[length(feats)]] |
|
|
if (!is.null(feat$geometry) && feat$geometry$type == "Polygon") { |
|
|
coords <- feat$geometry$coordinates[[1]] |
|
|
lngs <- vapply(coords, function(x) x[[1]], numeric(1)) |
|
|
lats <- vapply(coords, function(x) x[[2]], numeric(1)) |
|
|
rv$bbox <- c(min(lats), min(lngs), max(lats), max(lngs)) |
|
|
} |
|
|
} |
|
|
} |
|
|
}) |
|
|
observeEvent(input$clear_bbox, { |
|
|
rv$bbox <- NULL |
|
|
leafletProxy("select_map") %>% |
|
|
clearGroup("drawn_bboxes") %>% |
|
|
clearGroup("search_bbox") |
|
|
}) |
|
|
observeEvent(input$region_search_btn, { |
|
|
loc <- input$region_search |
|
|
if (!is.null(loc) && nzchar(loc)) { |
|
|
url <- paste0("https://nominatim.openstreetmap.org/search?format=json&q=", URLencode(loc)) |
|
|
res <- tryCatch(jsonlite::fromJSON(url), error=function(e) NULL) |
|
|
if (!is.null(res) && nrow(res) >= 1 && !is.null(res$boundingbox[1])) { |
|
|
bbox_bb <- res$boundingbox[1][[1]] |
|
|
if (is.character(bbox_bb) && length(bbox_bb) == 4) { |
|
|
bbox_raw <- as.numeric(bbox_bb) |
|
|
} else if (is.list(bbox_bb) && length(bbox_bb) == 4) { |
|
|
bbox_raw <- as.numeric(unlist(bbox_bb)) |
|
|
} else if (is.character(res$boundingbox[1])) { |
|
|
bbox_raw <- as.numeric(unlist(strsplit(res$boundingbox[1], ","))) |
|
|
} else { |
|
|
bbox_raw <- NULL |
|
|
} |
|
|
if (!is.null(bbox_raw) && length(bbox_raw) == 4 && all(!is.na(bbox_raw))) { |
|
|
bbox <- c(bbox_raw[1], bbox_raw[3], bbox_raw[2], bbox_raw[4]) |
|
|
leafletProxy("select_map") %>% |
|
|
clearGroup("search_bbox") %>% |
|
|
addRectangles( |
|
|
lng1 = bbox[2], lat1 = bbox[1], lng2 = bbox[4], lat2 = bbox[3], |
|
|
fillColor = "red", fillOpacity = 0.1, color = "red", group = "search_bbox" |
|
|
) %>% |
|
|
fitBounds(lng1 = bbox[2], lat1 = bbox[1], lng2 = bbox[4], lat2 = bbox[3]) |
|
|
rv$bbox <- bbox |
|
|
} else { |
|
|
showNotification("Unexpected bounding box format from geocoder.", type = "error", duration = 6) |
|
|
} |
|
|
} else { |
|
|
showNotification("Could not geocode this place. Try a different name.", type = "warning", duration = 5) |
|
|
} |
|
|
} |
|
|
}) |
|
|
output$bbox_coords <- renderText({ |
|
|
if (is.null(rv$bbox)) "No bounding box defined yet. Search for a place or draw a rectangle." else paste0( |
|
|
"Bounding box:\nSW: (", round(rv$bbox[1], 4), ", ", round(rv$bbox[2], 4), ")\nNE: (", round(rv$bbox[3], 4), ", ", round(rv$bbox[4], 4), ")") |
|
|
}) |
|
|
result_data <- reactiveVal(NULL) |
|
|
observeEvent(input$run_query, { |
|
|
req(input$date_range) |
|
|
req(rv$bbox) |
|
|
start_date <- as.Date(input$date_range[1]) |
|
|
end_date <- as.Date(input$date_range[2]) |
|
|
swlat <- rv$bbox[1]; swlng <- rv$bbox[2]; nelat <- rv$bbox[3]; nelng <- rv$bbox[4] |
|
|
if (input$data_source == "archived") { |
|
|
|
|
|
inat_all_raw <- arrow::read_parquet(parquet_path) |
|
|
inat_all <- inat_all_raw %>% |
|
|
filter(!is.na(latitude) & !is.na(longitude)) %>% |
|
|
filter(latitude >= swlat, latitude <= nelat, |
|
|
longitude >= swlng, longitude <= nelng) |> collect() |
|
|
if ("observed_on" %in% names(inat_all)) { |
|
|
inat_all <- inat_all %>% |
|
|
filter(!is.na(observed_on)) %>% |
|
|
filter(as.Date(observed_on) >= start_date, as.Date(observed_on) <= end_date) |
|
|
} |
|
|
if (input$query_type == "iconic" && !is.null(input$iconic_taxon) && input$iconic_taxon != "" && |
|
|
"iconic_taxon_name" %in% names(inat_all)) { |
|
|
inat_all <- inat_all %>% filter(iconic_taxon_name == input$iconic_taxon) |
|
|
} |
|
|
if (input$query_type == "species" && !is.null(input$species_name) && input$species_name != "" && |
|
|
"scientific_name" %in% names(inat_all)) { |
|
|
inat_all <- inat_all %>% filter(scientific_name == input$species_name) |
|
|
} |
|
|
hm <- get_high_mortality_days(inat_all) |
|
|
merged_high <- if (!is.null(hm$days)) inat_all %>% filter(as.Date(observed_on) %in% hm$days) else inat_all |
|
|
query_res <- list( |
|
|
merged_df_all = inat_all, |
|
|
merged_df = merged_high, |
|
|
daily_plot = make_daily_plot(inat_all, start_date, end_date), |
|
|
top_species_plot = make_top_species_plot(inat_all), |
|
|
map_hotspots_gg = make_hexbin_map(inat_all, start_date, end_date), |
|
|
daily_90th_quant = if (!is.null(hm$quant)) hm$quant else NA |
|
|
) |
|
|
result_data(query_res) |
|
|
} else { |
|
|
iconic_val <- if (input$query_type == "iconic") input$iconic_taxon else NULL |
|
|
species_val <- if (input$query_type == "species") input$species_name else NULL |
|
|
week_starts <- seq.Date(start_date, end_date, by = "1 week") |
|
|
showNotification( |
|
|
paste("Live Mode: About to fetch", length(week_starts), |
|
|
"weeks from iNaturalist API. This may take several minutes for large queries."), |
|
|
duration = 7, type = "warning" |
|
|
) |
|
|
progress <- shiny::Progress$new() |
|
|
on.exit(progress$close()) |
|
|
progress$set(message = paste("Live Query: Fetching", length(week_starts), "weeks"), value = 0) |
|
|
query_res <- getDeadVertebrates_dateRange( |
|
|
start_date = start_date, |
|
|
end_date = end_date, |
|
|
swlat = swlat, |
|
|
swlng = swlng, |
|
|
nelat = nelat, |
|
|
nelng = nelng, |
|
|
iconic_taxa = iconic_val, |
|
|
taxon_name = species_val, |
|
|
.shiny_progress = progress |
|
|
) |
|
|
result_data(query_res) |
|
|
} |
|
|
}) |
|
|
output$dailyPlot <- renderPlot({ req(result_data()); result_data()$daily_plot }) |
|
|
|
|
|
output$dailySummary <- renderText({ |
|
|
req(result_data()) |
|
|
df <- result_data()$merged_df_all |
|
|
if (nrow(df) == 0 || !"observed_on" %in% names(df)) return("No data available.") |
|
|
df <- df %>% mutate(obs_date = as.Date(observed_on)) %>% filter(!is.na(obs_date)) |
|
|
n_obs <- nrow(df) |
|
|
n_days <- n_distinct(df$obs_date) |
|
|
span_days <- if (n_days > 1) paste0(range(df$obs_date, na.rm=TRUE), collapse=" to ") else as.character(unique(df$obs_date)) |
|
|
counts_by_day <- df %>% count(obs_date) |
|
|
peak <- counts_by_day %>% filter(n == max(n)) %>% pull(obs_date) |
|
|
peak_val <- max(counts_by_day$n) |
|
|
avg_day <- round(mean(counts_by_day$n), 2) |
|
|
paste0( |
|
|
"Summary:\n", |
|
|
"- Total mortality records: ", n_obs, "\n", |
|
|
"- Date range: \n", span_days, "\n", |
|
|
"- Days with data: ", n_days, "\n", |
|
|
"- Average per day: ", avg_day, "\n", |
|
|
"- Peak day: ", paste(peak, collapse = ", "), " (", peak_val, " records)\n", |
|
|
if (peak_val > avg_day*2) "- Spike in mortality observations" else "" |
|
|
) |
|
|
|
|
|
}) |
|
|
|
|
|
output$speciesPlot <- renderPlot({ req(result_data()); result_data()$top_species_plot }) |
|
|
output$hotspotMap <- renderPlot({ req(result_data()); result_data()$map_hotspots_gg }) |
|
|
output$dataTable <- DT::renderDataTable({ |
|
|
req(result_data()) |
|
|
df <- result_data()$merged_df_all |
|
|
if (nrow(df) == 0) { |
|
|
return(DT::datatable(data.frame(Message = "No records found"), options = list(pageLength = 20))) |
|
|
} |
|
|
|
|
|
if (!"scientific_name" %in% names(df) && "taxon.name" %in% names(df)) { |
|
|
df$scientific_name <- df$taxon.name |
|
|
} |
|
|
|
|
|
if ("id" %in% names(df)) { |
|
|
df$inat_link <- paste0("<a href='https://www.inaturalist.org/observations/", df$id, "' target='_blank'>", df$id, "</a>") |
|
|
} else { |
|
|
df$inat_link <- NA |
|
|
} |
|
|
|
|
|
df$image_thumb <- "No Img" |
|
|
if ("image_url" %in% names(df)) { |
|
|
df$image_thumb <- ifelse(!is.na(df$image_url) & df$image_url != "", paste0("<img src='", df$image_url, "' width='50'/>"), "No Img") |
|
|
} else if ("taxon.default_photo.square_url" %in% names(df)) { |
|
|
df$image_thumb <- ifelse(!is.na(df$taxon.default_photo.square_url) & df$taxon.default_photo.square_url != "", paste0("<img src='", df$taxon.default_photo.square_url, "' width='50'/>"), "No Img") |
|
|
} else if ("taxon" %in% names(df)) { |
|
|
taxon_photo <- sapply(df$taxon, function(x) { |
|
|
if (is.list(x) && "default_photo" %in% names(x) && !is.null(x$default_photo$square_url)) x$default_photo$square_url else NA |
|
|
}) |
|
|
df$image_thumb <- ifelse(!is.na(taxon_photo) & taxon_photo != "", paste0("<img src='", taxon_photo, "' width='50'/>"), "No Img") |
|
|
} |
|
|
|
|
|
show_cols <- c( |
|
|
"inat_link", "image_thumb", |
|
|
"scientific_name", |
|
|
intersect(c("observed_on", "created_at_details.date"), names(df)), |
|
|
"latitude", "longitude", |
|
|
setdiff(names(df), c("inat_link", "image_thumb", "scientific_name", "observed_on", "created_at_details.date", "latitude", "longitude")) |
|
|
) |
|
|
DT::datatable(df[, show_cols[show_cols %in% names(df)], drop = FALSE], escape = FALSE, |
|
|
options = list(pageLength = 20, autoWidth = TRUE)) |
|
|
}) |
|
|
output$downloadAll <- downloadHandler( |
|
|
filename = function() paste0("inat_dead_ALL_", Sys.Date(), ".csv"), |
|
|
content = function(file) { req(result_data()); readr::write_csv(result_data()$merged_df_all, file) } |
|
|
) |
|
|
} |
|
|
|
|
|
shinyApp(ui = ui, server = server) |
|
|
|
