Update Shiny app with latest app.R and config

app.R

@@ -1,36 +1,18 @@
 ##################################################################
-# Single R Script: Mortality Analysis + Shiny - Two-Click BBox
-# Using Weekly Queries (No Hard-Coded Years)
+# Dead Wildlife iNaturalist Shiny – Professional Version (Live/Archive, All Data Table Fixed)
 ##################################################################
 
-# See https://www.inaturalist.org/pages/api+recommended+practices
-# Query Rate
-# Please keep requests to about 1 per second, and around 10k API requests a day
-# The API is meant to be used for building applications and for fetching small to medium batches of data. It is not meant to be a way to download data in bulk
-# Requests exceeding this limit might be throttled, and will return an HTTP 429 exception “Too Many Requests”
-# Please add delays into your code to keep under these limits, and especially if you’re getting 429 errors
-# We may block IPs that consistently exceed these limits
-# Please use a single IP address for fetching data. If we think multiple IPs are being used in coordination to bypass rate limits, we may block those IPs regardless of query rate
-# Downloading over 5 GB of media per hour or 24 GB of media per day may result in a permanent block
-# If writing software to interact with the API, please consider using a custom User Agent to identify your application, or iNaturalist username, or something we might use to differentiate your requests
-# The User Agent can be set with an HTTP header, e.g. User-Agent: [[application or user name]
-#
-
-### 1) Install/Load Required Packages ####
+# Install and load required packages
 required_packages <- c(
   "httr", "jsonlite", "tidyverse", "glue", "lubridate",
-  "wesanderson", "viridis", "shinycssloaders",
+  "wesanderson", "viridis", "hexbin", "shinycssloaders",
   "DT", "maps", "mapdata", "leaflet", "leaflet.extras",
-  "shinythemes", "shiny"
+  "shinythemes", "shiny", "arrow"
 )
-
 installed_packages <- rownames(installed.packages())
 for (pkg in required_packages) {
-  if (!pkg %in% installed_packages) {
-    install.packages(pkg, dependencies = TRUE)
-  }
+  if (!pkg %in% installed_packages) install.packages(pkg, dependencies = TRUE)
 }
-
 library(httr)
 library(jsonlite)
 library(tidyverse)
@@ -38,6 +20,7 @@ library(glue)
 library(lubridate)
 library(wesanderson)
 library(viridis)
+library(hexbin)
 library(shinycssloaders)
 library(DT)
 library(maps)
@@ -46,284 +29,234 @@ library(leaflet)
 library(leaflet.extras)
 library(shinythemes)
 library(shiny)
+library(arrow)
+
+# Path to your archived parquet file (update if needed)
+# parquet_path <- "~/inat_all_Apr122025.parquet"
+parquet_path <- "https://huggingface.co/datasets/diegoellissoto/iNaturalist_mortality_records_12Apr2025/resolve/main/inat_all_Apr122025.parquet"
+# ------------------- Helper Functions ---------------------
+make_daily_plot <- function(df, start_date, end_date) {
+  if (!"observed_on" %in% names(df)) return(ggplot() + theme_void() + labs(title = "No date info"))
+  if (nrow(df) == 0) return(ggplot() + theme_void() + labs(title = "No data"))
+  df <- df %>%
+    mutate(obs_date = as.Date(observed_on),
+           Window   = format(obs_date, "%Y")) %>%
+    filter(!is.na(obs_date))
+  counts_by_day <- df %>%
+    group_by(Window, obs_date) %>%
+    summarise(n = n_distinct(id), .groups = "drop")
+  y_max_value <- max(counts_by_day$n, na.rm = TRUE)
+  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))
+}
 
-##################################################################
-# 2) Mortality-Analysis Functions
-##################################################################
+make_top_species_plot <- function(df) {
+  if (!"scientific_name" %in% names(df)) return(ggplot() + theme_void() + labs(title = "No species info"))
+  if (nrow(df) == 0) return(ggplot() + theme_void() + labs(title = "No data"))
+  df <- df %>%
+    mutate(obs_date = as.Date(observed_on),
+           Window   = format(obs_date, "%Y"))
+  species_counts <- df %>%
+    filter(!is.na(scientific_name)) %>%
+    group_by(Window, scientific_name) %>%
+    summarise(dead_count = n(), .groups = "drop")
+  top_species_overall <- species_counts %>%
+    group_by(scientific_name) %>%
+    summarise(total_dead = sum(dead_count)) %>%
+    arrange(desc(total_dead)) %>%
+    slice_head(n = 20)
+  species_top20 <- species_counts %>%
+    filter(scientific_name %in% top_species_overall$scientific_name)
+  ggplot(species_top20, aes(
+    x   = reorder(scientific_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)
+}
 
-# -- Base function to fetch dead observations over a specified date range --
+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 = "plasma", name = "Observation Count") +
+    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)
+}
+
+# -- API Fetch/Progress bar logic (Live mode) --
 fetch_dead_data_once <- function(
-    place_id    = NULL,
-    swlat       = NULL,
-    swlng       = NULL,
-    nelat       = NULL,
-    nelng       = NULL,
-    start_date,
-    end_date,
-    iconic_taxa = NULL,
-    taxon_name  = NULL,
-    conservation_status = NULL,
-    per_page    = 200,
-    max_pages   = 200
+    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",               # 'Dead' annotation
-    "term_value_id=19",         # 'Dead' annotation
-    "verifiable=true",          # only verifiable
-    glue("d1={start_date}"),    # start date
-    glue("d2={end_date}"),      # end date
-    "order=desc",
-    "order_by=created_at",
-    glue("per_page={per_page}")
+    "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)}"))
-  }
-
-  if (!is.null(conservation_status) && conservation_status != "") {
-    # If you'd like to filter by iNat conservation status,
-    # or e.g. pass additional parameters to the API
-    if (!grepl("=", conservation_status, fixed = TRUE)) {
-      q_parts <- c(q_parts, glue("cs={URLencode(conservation_status)}"))
-    } else {
-      q_parts <- c(q_parts, conservation_status)
-    }
-  }
-
+  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 = "&")
-
-  # Build location portion of query
-  loc_part <- ""
-  if (!is.null(place_id)) {
-    loc_part <- glue("&place_id={place_id}")
-  } else if (!is.null(swlat) && !is.null(swlng) &&
-             !is.null(nelat) && !is.null(nelng)) {
-    loc_part <- glue("&nelat={nelat}&nelng={nelng}&swlat={swlat}&swlng={swlng}")
-  } else {
-    stop("Must provide either 'place_id' OR bounding box (swlat, swlng, nelat, nelng).")
-  }
-
+  loc_part <- glue("&nelat={nelat}&nelng={nelng}&swlat={swlat}&swlng={swlng}")
   observations_list <- list()
   current_page <- 1
-
   while (current_page <= max_pages) {
-    query_url <- paste0(
-      base_url, "?", query_params, "&page=", current_page, loc_part
-    )
-
-    message("Fetching page ", current_page,
-            " [", start_date, " to ", end_date, "]:\n", query_url)
-
+    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$results) == 0) {
-      message("No more results at page ", current_page)
-      break
-    }
-
+    if (length(parsed$results) == 0) break
     obs_page_df <- as_tibble(parsed$results)
     observations_list[[current_page]] <- obs_page_df
-
-    # If the returned page is smaller than per_page, we've reached the last page
-    if (nrow(obs_page_df) < per_page) {
-      message("Reached last page of results at page ", current_page)
-      break
-    }
-
+    if (nrow(obs_page_df) < per_page) break
     current_page <- current_page + 1
-    Sys.sleep(1.5)  # Polite pause
+    Sys.sleep(1.4)
   }
-
-  observations_all <- bind_rows(observations_list)
-  return(observations_all)
+  bind_rows(observations_list)
 }
 
-# -- Function to fetch data by iterating through each WEEK of a given year --
-fetch_dead_data_weekly <- function(
-    year,
-    place_id    = NULL,
-    swlat       = NULL,
-    swlng       = NULL,
-    nelat       = NULL,
-    nelng       = NULL,
-    iconic_taxa = NULL,
-    taxon_name  = NULL,
-    conservation_status = NULL,
-    per_page    = 200,
-    max_pages   = 200
+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_of_year <- as.Date(glue("{year}-01-01"))
-  end_of_year   <- as.Date(glue("{year}-12-31"))
-
-  # Create a sequence of "week starts" from Jan 1 to Dec 31
-  week_starts <- seq.Date(start_of_year, end_of_year, by = "1 week")
-
-  weekly_list <- list()
-
+  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)) {
-    start_date <- week_starts[i]
-    # If not the last index, end_date = next start - 1 day, else clamp to year-end
-    if (i < length(week_starts)) {
-      end_date <- week_starts[i + 1] - 1
-    } else {
-      end_date <- end_of_year
+    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}")
+      )
     }
-
-    message("\n--- Querying ", year, ", Week #", i,
-            " [", start_date, " to ", end_date, "] ---")
-
     df_week <- fetch_dead_data_once(
-      place_id    = place_id,
-      swlat       = swlat,
-      swlng       = swlng,
-      nelat       = nelat,
-      nelng       = nelng,
-      start_date  = start_date,
-      end_date    = end_date,
-      iconic_taxa = iconic_taxa,
-      taxon_name  = taxon_name,
-      conservation_status = conservation_status,
-      per_page    = per_page,
-      max_pages   = max_pages
+      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
     )
-    weekly_list[[i]] <- df_week
-
-    Sys.sleep(1.5)
-  }
-
-  year_df <- bind_rows(weekly_list)
-  return(year_df)
-}
-
-# -- Wrapper that iterates over multiple years, pulling data weekly for each year --
-getDeadVertebrates_weeklyLoop <- function(
-    years,                 # <--- No default: pass your own vector of years
-    place_id              = NULL,
-    swlat                 = NULL,
-    swlng                 = NULL,
-    nelat                 = NULL,
-    nelng                 = NULL,
-    iconic_taxa           = NULL,
-    taxon_name            = NULL,
-    conservation_status   = NULL,
-    per_page              = 500,
-    max_pages             = 500,
-    outdir                = NULL
-) {
-  all_years_list <- list()
-
-  # For each year, run weekly fetch
-  for (yr in years) {
-    message("\n========= YEAR: ", yr, " ==========\n")
-    yr_df <- fetch_dead_data_weekly(
-      year       = yr,
-      place_id   = place_id,
-      swlat      = swlat,
-      swlng      = swlng,
-      nelat      = nelat,
-      nelng      = nelng,
-      iconic_taxa= iconic_taxa,
-      taxon_name = taxon_name,
-      conservation_status = conservation_status,
-      per_page   = per_page,
-      max_pages  = max_pages
-    ) %>%
-      mutate(Window = as.character(yr))
-
-    all_years_list[[as.character(yr)]] <- yr_df
+    all_weeks_list[[i]] <- df_week
+    Sys.sleep(1.4)
   }
-
-  merged_df_all <- bind_rows(all_years_list)
-
-  # If no data found or missing crucial columns, create empty placeholders
-  if (!"created_at_details.date" %in% names(merged_df_all) ||
-      nrow(merged_df_all) == 0) {
-    daily_plot <- ggplot() +
-      labs(title = "No 'Dead' Observations Found", x = NULL, y = NULL) +
-      theme_void()
-
-    top_species_plot <- ggplot() +
-      labs(title = "No species data", x = NULL, y = NULL) +
-      theme_void()
-
-    map_hotspots_gg <- ggplot() +
-      labs(title = "No data for hotspots map") +
-      theme_void()
-
+  merged_df_all <- bind_rows(all_weeks_list)
+  # Everything else unchanged (see previous versions, e.g. make plots, high mortality)
+  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       = daily_plot,
-      top_species_plot = top_species_plot,
-      map_hotspots_gg  = map_hotspots_gg,
+      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
     ))
   }
-
-  # Optionally write out to disk
-  if (!is.null(outdir)) {
-    if (!dir.exists(outdir)) {
-      dir.create(outdir, recursive = TRUE)
-    }
-    readr::write_csv(merged_df_all, file.path(outdir, "merged_df_ALL_data.csv"))
-  }
-
-  # Aggregate counts by day
+  merged_df_all <- merged_df_all %>%
+    mutate(obs_date = as.Date(observed_on),
+           Window   = format(obs_date, "%Y"))
   counts_by_day <- merged_df_all %>%
-    mutate(obs_date = as.Date(`observed_on`)) %>%
     group_by(Window, obs_date) %>%
     summarise(n = n_distinct(id), .groups = "drop")
-
   y_max_value <- max(counts_by_day$n, na.rm = TRUE)
-   n_windows   <- length(unique(counts_by_day$Window))
-   wes_colors  <- wes_palette("Zissou1", n_windows, type = "discrete")
-
-  # Daily line plot
   daily_plot <- ggplot(counts_by_day, aes(x = obs_date, y = n, color = Window)) +
     geom_line(size = 1.2) +
     geom_point(size = 2) +
-    # scale_color_viridis_d() +
-    scale_x_date(date_labels = "%b", date_breaks = "1 month") +
+    scale_x_date(date_labels = "%b %d", date_breaks = "1 month") +
     scale_y_continuous(limits = c(0, y_max_value)) +
     labs(
-      title = glue("Daily 'Dead' Observations (Years {paste(years, collapse=', ')})"),
-      x     = "Month",
+      title = glue("Daily 'Dead' Observations ({start_date} to {end_date})"),
+      x     = "Date",
       y     = "Number of Observations",
       color = "Year"
     ) +
     theme_minimal(base_size = 14) +
     theme(axis.text.x = element_text(angle = 45, hjust = 1))
-
-  # Top species bar plot
   if ("taxon.name" %in% names(merged_df_all)) {
     species_counts <- merged_df_all %>%
       filter(!is.na(taxon.name)) %>%
       group_by(Window, taxon.name) %>%
       summarise(dead_count = n(), .groups = "drop")
-
     top_species_overall <- species_counts %>%
       group_by(taxon.name) %>%
       summarise(total_dead = sum(dead_count)) %>%
       arrange(desc(total_dead)) %>%
       slice_head(n = 20)
-
     species_top20 <- species_counts %>%
       filter(taxon.name %in% top_species_overall$taxon.name)
-
     top_species_plot <- ggplot(species_top20, aes(
       x   = reorder(taxon.name, -dead_count),
       y   = dead_count,
@@ -331,8 +264,6 @@ getDeadVertebrates_weeklyLoop <- function(
     )) +
       geom_col(position = position_dodge(width = 0.7)) +
       coord_flip() +
-      # scale_fill_manual(values = wes_colors) +
-      # scale_color_viridis_d() +
       labs(
         title = "Top 20 Species with 'Dead' Observations",
         x     = "Species",
@@ -345,71 +276,51 @@ getDeadVertebrates_weeklyLoop <- function(
       labs(title = "No 'taxon.name' column found", x = NULL, y = NULL) +
       theme_void()
   }
-
-  # Identify "high mortality" days (>= 90th percentile)
   daily_quantile <- quantile(counts_by_day$n, probs = 0.90, na.rm = TRUE)
   high_mortality_days <- counts_by_day %>%
     filter(n >= daily_quantile) %>%
     pull(obs_date)
-
   merged_high <- merged_df_all %>%
-    mutate(obs_date = as.Date(`observed_on`)) %>%
     filter(obs_date %in% high_mortality_days)
-
-  # Map of top-90% mortality days
-  if ("location" %in% names(merged_high)) {
-    location_df <- merged_high %>%
+  if ("location" %in% names(merged_df_all)) {
+    location_df_all <- merged_df_all %>%
       filter(!is.na(location) & location != "") %>%
       separate(location, into = c("lat_str", "lon_str"), sep = ",", remove = FALSE) %>%
-      mutate(
-        latitude  = as.numeric(lat_str),
-        longitude = as.numeric(lon_str)
-      )
-
-    if (nrow(location_df) == 0) {
+      mutate(latitude = as.numeric(lat_str), longitude = as.numeric(lon_str))
+    if (nrow(location_df_all) == 0) {
       map_hotspots_gg <- ggplot() +
-        labs(title = "No data in top 90th percentile days with valid location") +
+        labs(title = "No spatial data available for map") +
         theme_void()
     } else {
-      min_lon <- min(location_df$longitude, na.rm = TRUE)
-      max_lon <- max(location_df$longitude, na.rm = TRUE)
-      min_lat <- min(location_df$latitude,  na.rm = TRUE)
-      max_lat <- max(location_df$latitude,  na.rm = TRUE)
-
-      map_hotspots_gg <- ggplot(location_df, aes(x = longitude, y = latitude, color = Window)) +
+      x_limits <- range(location_df_all$longitude, na.rm = TRUE)
+      y_limits <- range(location_df_all$latitude,  na.rm  = TRUE)
+      map_hotspots_gg <- ggplot() +
         borders("world", fill = "gray80", colour = "white") +
-        geom_point(alpha = 0.6, size = 2) +
-        # scale_color_viridis_d() +
-        coord_quickmap(
-          xlim = c(min_lon, max_lon),
-          ylim = c(min_lat, max_lat),
-          expand = TRUE
+        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("Top 90th percentile mortality days ({paste(years, collapse=', ')})"),
-          x     = "Longitude",
-          y     = "Latitude",
-          color = "Year"
+          title = glue("'Dead' Wildlife Hexbin Map ({start_date} to {end_date})"),
+          x = "Longitude",
+          y = "Latitude"
         ) +
-        theme_minimal(base_size = 14)
+        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 top 90% days map") +
+      labs(title = "No 'location' column for map") +
       theme_void()
   }
-
-  # Optionally save outputs
-  if (!is.null(outdir)) {
-    readr::write_csv(merged_high, file.path(outdir, "merged_df_top90.csv"))
-    ggsave(file.path(outdir, "daily_plot.png"),
-           daily_plot, width = 8, height = 5, dpi = 300)
-    ggsave(file.path(outdir, "top_species_plot.png"),
-           top_species_plot, width = 7, height = 7, dpi = 300)
-    ggsave(file.path(outdir, "map_hotspots.png"),
-           map_hotspots_gg, width = 8, height = 5, dpi = 300)
-  }
-
   return(list(
     merged_df_all    = merged_df_all,
     merged_df        = merged_high,
@@ -419,353 +330,346 @@ getDeadVertebrates_weeklyLoop <- function(
     daily_90th_quant = daily_quantile
   ))
 }
-
-##################################################################
-# 3) Shiny App: UI + Server (Weekly Queries)
-##################################################################
-
+# ------------------------ UI --------------------------
 ui <- fluidPage(
-  theme = shinytheme("cosmo"),  # Use a professional theme from shinythemes
-
-  # -- Logo and Title at the top --
+  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")
-    )
+    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",
-
-        # == Query Panel ==
-        tabPanel(
-          title = "Query",
-          br(),
-          radioButtons("region_mode", "Region Input Mode:",
-                       choices = c("Enter Numeric place_id"   = "place",
-                                   "Two-Click Bounding Box"    = "bbox"),
-                       # choices = c(
-                       # "Two-Click Bounding Box"    = "bbox"),
-                       selected = "bbox"),
-
-          # If user chooses numeric "place_id"
-          conditionalPanel(
-            condition = "input.region_mode == 'place'",
-            numericInput("place_id",
-                         "Numeric place_id (e.g. 1 = USA, 6712 = Canada, 14 = California)",
-                         value = 1, min = 1, max = 999999, step = 1)
-          ),
-
-          # If user chooses bounding box
-          conditionalPanel(
-            condition = "input.region_mode == 'bbox'",
-            helpText("Left-click once for the SW corner, once more for the NE corner."),
-            leafletOutput("map_two_click", height = "300px"),
-            br(),
-            actionButton("clear_bbox", "Clear bounding box"),
-            br(), br(),
-            verbatimTextOutput("bbox_coords")
-          ),
-
-          # Years
-          checkboxGroupInput("years", "Select Year(s):",
-                             choices = 2018:2025,
-                             selected = c(2022, 2023)),
-
-          # Query by iconic class or exact species
-          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("downloadTop90", "Download Top-90% CSV", icon = icon("download")),
-          br(), br(),
-          downloadButton("downloadAll",   "Download ALL Data CSV", icon = icon("download"))
-        ),
-
-        # == About Panel ==
-        tabPanel(
-          title = "About",
-          br(),
-          p("This Shiny application was created by Diego Ellis Soto (UC Berkeley).
-            It queries iNaturalist for observations that have been annotated as 'Dead' wildlife (term_id=17, term_value_id=19).
-            The data is fetched via the iNaturalist API and summarized here for scientific or conservation purposes.")
-        ),
-
-        # == Participatory Science Panel ==
-        tabPanel(
-          title = "Participatory Science",
-          br(),
-          p("Citizen science platforms like iNaturalist allow everyday people to collect and share data about local biodiversity.
-            Recording observations of dead wildlife can help track mortality events, disease spread, and other factors affecting animal populations."),
-          p("We encourage everyone to contribute their sightings responsibly, ensuring that any data on roadkill or other mortalities can help conservation efforts and
-            raise public awareness.")
-        ),
-
-        # == How To Use Panel ==
-        tabPanel(
-          title = "How to Use",
-          br(),
-          p("This application lets you retrieve data about dead wildlife observations from iNaturalist.
-            You can choose to manually provide a numeric place_id or define a custom bounding box by clicking twice on the map."),
-          p("You can also decide whether to query by taxon class (e.g. Aves) or by exact species name (e.g. Puma concolor)."),
-          p("After selecting your inputs, press 'Run Query.' Two separate CSV downloads are provided: (1) for all data retrieved, and (2) for only the top-90% mortality days (for hotspot analysis).")
-        )
+      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$p("For questions or feedback, visit our GitHub repository or email the authors.")
+                  )
       )
     ),
-
     mainPanel(
       tabsetPanel(
-        tabPanel("Daily Time Series",    withSpinner(plotOutput("dailyPlot"), type = 6)),
-        tabPanel("Top Species",          withSpinner(plotOutput("speciesPlot"), type = 6)),
-        tabPanel("Hotspots Map (90th%)", withSpinner(plotOutput("hotspotMap"), type = 6)),
-        tabPanel("Data Table (Top-90%)", withSpinner(DT::dataTableOutput("dataTable"), type = 6))
+        # ----------- CHANGED: summary beside plot -----------
+        tabPanel("Daily Time Series",
+                 fluidRow(
+                   column(width = 8, withSpinner(plotOutput("dailyPlot"), type = 6)),
+                   column(width = 4, verbatimTextOutput("dailySummary"))
+                 )
+        ),
+        tabPanel("Top Species",           withSpinner(plotOutput("speciesPlot"), type = 6)),
+        tabPanel("Hexbin Map (All Data)", withSpinner(plotOutput("hotspotMap"),  type = 6)),
+        tabPanel("All Data Table",        withSpinner(DT::dataTableOutput("dataTable"), type = 6))
       )
     )
   )
 )
-
+# -------------------- SERVER --------------------------
 server <- function(input, output, session) {
-
-  # Reactive values for bounding box corners
-  rv <- reactiveValues(
-    corner1 = NULL,
-    corner2 = NULL,
-    bbox    = NULL
-  )
-
-  # Initialize map
-  output$map_two_click <- renderLeaflet({
-    leaflet() %>%
-      addTiles() %>%
-      setView(lng = -100, lat = 40, zoom = 4)
+  rv <- reactiveValues(bbox = NULL)
+  output$select_map <- renderLeaflet({
+    leaflet() %>% addTiles() %>%
+      setView(lng = -95, lat = 40, zoom = 3) %>%
+      addDrawToolbar(
+        targetGroup = "drawn_bboxes",
+        rectangleOptions = drawRectangleOptions(repeatMode = FALSE),
+        polylineOptions = FALSE, circleOptions = FALSE,
+        markerOptions = FALSE, circleMarkerOptions = FALSE,
+        polygonOptions = FALSE, editOptions = editToolbarOptions()
+      )
   })
-
-  # Handle bounding box clicks
-  observeEvent(input$map_two_click_click, {
-    req(input$region_mode == "bbox")
-
-    click <- input$map_two_click_click
-    if (is.null(click)) return()
-
-    lat_clicked <- click$lat
-    lng_clicked <- click$lng
-
-    if (is.null(rv$corner1)) {
-      rv$corner1 <- c(lat_clicked, lng_clicked)
-      showNotification("First corner set. Now click for the opposite corner.")
-
-      leafletProxy("map_two_click") %>%
-        clearMarkers() %>%
-        addMarkers(lng = lng_clicked, lat = lat_clicked, popup = "Corner 1")
-
-      rv$corner2 <- NULL
-      rv$bbox    <- NULL
-
-    } else {
-      rv$corner2 <- c(lat_clicked, lng_clicked)
-
-      lat_min <- min(rv$corner1[1], rv$corner2[1])
-      lat_max <- max(rv$corner1[1], rv$corner2[1])
-      lng_min <- min(rv$corner1[2], rv$corner2[2])
-      lng_max <- max(rv$corner1[2], rv$corner2[2])
-
-      rv$bbox <- c(lat_min, lng_min, lat_max, lng_max)
-
-      showNotification("Second corner set. Bounding box defined!", duration = 2)
-
-      leafletProxy("map_two_click") %>%
-        clearMarkers() %>%
-        addMarkers(lng = rv$corner1[2], lat = rv$corner1[1], popup = "Corner 1") %>%
-        addMarkers(lng = rv$corner2[2], lat = rv$corner2[1], popup = "Corner 2") %>%
-        clearShapes() %>%
-        addRectangles(
-          lng1 = lng_min, lat1 = lat_min,
-          lng2 = lng_max, lat2 = lat_max,
-          fillColor = "red", fillOpacity = 0.2,
-          color = "red"
-        )
+  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$clear_bbox, {
-    rv$corner1 <- NULL
-    rv$corner2 <- NULL
-    rv$bbox    <- NULL
-
-    leafletProxy("map_two_click") %>%
-      clearMarkers() %>%
-      clearShapes()
+    rv$bbox <- NULL
+    leafletProxy("select_map") %>%
+      clearGroup("drawn_bboxes") %>%
+      clearGroup("search_bbox")
   })
-
-  output$bbox_coords <- renderText({
-    req(input$region_mode == "bbox")
-
-    if (is.null(rv$bbox)) {
-      "No bounding box defined yet."
-    } else {
-      paste0(
-        "Bounding box:\n",
-        "SW corner: (", rv$bbox[1], ", ", rv$bbox[2], ")\n",
-        "NE corner: (", rv$bbox[3], ", ", rv$bbox[4], ")"
-      )
+  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$bbox <- bbox
+        } else {
+          showNotification("Unexpected bounding box format from geocoder.", type = "error", duration = 6)
+        }
+      } else {
+        showNotification("Could not geocode this place. Try a different name.", type = "warning", duration = 5)
+      }
     }
   })
-
-  # Store final query results
+  output$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$bbox[4], 4), ")")
+  })
   result_data <- reactiveVal(NULL)
-
-  # Main "Run Query" button
   observeEvent(input$run_query, {
-    req(input$years)
-    shiny::validate(need(length(input$years) > 0, "Please select at least one year."))
-
-    yrs <- as.numeric(input$years)
-
-    # Region logic
-    place_id_val <- NULL
-    swlat_val <- NULL
-    swlng_val <- NULL
-    nelat_val <- NULL
-    nelng_val <- NULL
-
-    if (input$region_mode == "place") {
-      place_id_val <- input$place_id
-    } else {
-      shiny::validate(need(!is.null(rv$bbox), "Please click twice on the map to define bounding box."))
-      swlat_val <- rv$bbox[1]
-      swlng_val <- rv$bbox[2]
-      nelat_val <- rv$bbox[3]
-      nelng_val <- rv$bbox[4]
-    }
-
-    # Query type logic
-    iconic_val <- NULL
-    species_val <- NULL
-    if (input$query_type == "iconic") {
-      iconic_val <- input$iconic_taxon
+    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$data_source == "archived") {
+      # req(file.exists(parquet_path))
+      inat_all_raw <- arrow::read_parquet(parquet_path)#  %>% as_tibble()
+      inat_all <- inat_all_raw %>%
+        filter(!is.na(latitude) & !is.na(longitude)) %>%
+        filter(latitude  >= swlat, latitude  <= nelat,
+               longitude >= swlng, longitude <= nelng) |> collect()
+      if ("observed_on" %in% names(inat_all)) {
+        inat_all <- inat_all %>%
+          filter(!is.na(observed_on)) %>%
+          filter(as.Date(observed_on) >= start_date, as.Date(observed_on) <= end_date)
+      }
+      if (input$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$quant else NA
+      )
+      result_data(query_res)
     } else {
-      species_val <- input$species_name
-    }
-
-    # Fetch data
-    withProgress(message = 'Fetching data from iNaturalist (Weekly)...', value = 0, {
-      incProgress(0.4)
-
-      query_res <- getDeadVertebrates_weeklyLoop(
-        years        = yrs,
-        place_id     = place_id_val,
-        swlat        = swlat_val,
-        swlng        = swlng_val,
-        nelat        = nelat_val,
-        nelng        = nelng_val,
-        iconic_taxa  = iconic_val,
-        taxon_name   = species_val
+      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$set(message = paste("Live Query: Fetching", length(week_starts), "weeks"), value = 0)
+      query_res <- getDeadVertebrates_dateRange(
+        start_date    = start_date,
+        end_date      = end_date,
+        swlat         = swlat,
+        swlng         = swlng,
+        nelat         = nelat,
+        nelng         = nelng,
+        iconic_taxa   = iconic_val,
+        taxon_name    = species_val,
+        .shiny_progress = progress
       )
-
       result_data(query_res)
-      incProgress(1)
-    })
-  })
-
-  # Output plots
-  output$dailyPlot <- renderPlot({
-    req(result_data())
-    result_data()$daily_plot
-  })
-
-  output$speciesPlot <- renderPlot({
-    req(result_data())
-    result_data()$top_species_plot
+    }
   })
-
-  output$hotspotMap <- renderPlot({
+  output$dailyPlot   <- renderPlot({ req(result_data()); result_data()$daily_plot })
+  
+  output$dailySummary <- renderText({
     req(result_data())
-    result_data()$map_hotspots_gg
+    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 data table (top-90% subset)
+  
+  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   # top 90% subset
-
+    df <- result_data()$merged_df_all
     if (nrow(df) == 0) {
-      return(DT::datatable(
-        data.frame(Message = "No records found"),
-        options = list(pageLength = 20) # Show 20 records
-      ))
+      return(DT::datatable(data.frame(Message = "No records found"), options = list(pageLength = 20)))
     }
-
-    df <- df %>%
-      mutate(
-        inat_link = paste0(
-          "<a href='https://www.inaturalist.org/observations/",
-          id, "' target='_blank'>", id, "</a>"
-        )
-      )
-
-    photo_col <- "taxon.default_photo.square_url"
-    if (photo_col %in% names(df)) {
-      df$image_thumb <- ifelse(
-        !is.na(df[[photo_col]]) & df[[photo_col]] != "",
-        paste0("<img src='", df[[photo_col]], "' width='50'/>"),
-        "No Img"
-      )
+    # --- Fix column naming for scientific_name ---
+    if (!"scientific_name" %in% names(df) && "taxon.name" %in% names(df)) {
+      df$scientific_name <- df$taxon.name
+    }
+    # --- Add inat_link ---
+    if ("id" %in% names(df)) {
+      df$inat_link <- paste0("<a href='https://www.inaturalist.org/observations/", df$id, "' target='_blank'>", df$id, "</a>")
     } else {
-      df$image_thumb <- "No Img"
+      df$inat_link <- NA
     }
-
+    # --- Fix image column (robust to both sources) ---
+    df$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 columns ---
     show_cols <- c(
-      "inat_link", "image_thumb", "taxon.name", "created_at_details.date",
-      setdiff(names(df), c("inat_link", "image_thumb", "taxon.name", "created_at_details.date"))
-    )
-
-    DT::datatable(
-      df[, show_cols, drop = FALSE],
-      escape = FALSE,
-      options = list(pageLength = 20, autoWidth = TRUE) # Page 50 prior
+      "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))
   })
-
-  # Download handlers
-  output$downloadTop90 <- downloadHandler(
-    filename = function() {
-      paste0("inat_dead_top90_", Sys.Date(), ".csv")
-    },
-    content = function(file) {
-      req(result_data())
-      readr::write_csv(result_data()$merged_df, file)
-    }
-  )
-
   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)
-    }
+    filename = function() paste0("inat_dead_ALL_", Sys.Date(), ".csv"),
+    content = function(file) { req(result_data()); readr::write_csv(result_data()$merged_df_all, file) }
   )
 }
 

poc/app_no90_2025.R

@@ -0,0 +1,801 @@
+# Remove mapping 9% and replaced it with a hexbin map
+# Remove download option for 90% percentile of data
+# Polish the About and How to section
+# Remove Data Table (Top 90%) in title and replace it with all the data as well!
+
+# Optional: Either incorporate past mortality data or just upload in zenodo
+# Optional: Date slider
+
+##################################################################
+# Single R Script: Mortality Analysis + Shiny - Hexbin Map (All Data)
+# Using Weekly Queries (No Hard-Coded Years)
+##################################################################
+
+# See https://www.inaturalist.org/pages/api+recommended+practices
+# Query Rate
+# Please keep requests to about 1 per second, and around 10k API requests a day
+# The API is meant to be used for building applications and for fetching small to medium batches of data. It is not meant to be a way to download data in bulk
+# Requests exceeding this limit might be throttled, and will return an HTTP 429 exception “Too Many Requests”
+# Please add delays into your code to keep under these limits, and especially if you’re getting 429 errors
+# We may block IPs that consistently exceed these limits
+# Please use a single IP address for fetching data. If we think multiple IPs are being used in coordination to bypass rate limits, we may block those IPs regardless of query rate
+# Downloading over 5 GB of media per hour or 24 GB of media per day may result in a permanent block
+# If writing software to interact with the API, please consider using a custom User Agent to identify your application, or iNaturalist username, or something we might use to differentiate your requests
+# The User Agent can be set with an HTTP header, e.g. User-Agent: [[application or user name]
+
+### 1) Install/Load Required Packages ####
+required_packages <- c(
+  "httr", "jsonlite", "tidyverse", "glue", "lubridate",
+  "wesanderson", "viridis", "hexbin", "shinycssloaders",
+  "DT", "maps", "mapdata", "leaflet", "leaflet.extras",
+  "shinythemes", "shiny"
+)
+
+installed_packages <- rownames(installed.packages())
+for (pkg in required_packages) {
+  if (!pkg %in% installed_packages) {
+    install.packages(pkg, dependencies = TRUE)
+  }
+}
+
+library(httr)
+library(jsonlite)
+library(tidyverse)
+library(glue)
+library(lubridate)
+library(wesanderson)
+library(viridis)
+library(hexbin)
+library(shinycssloaders)
+library(DT)
+library(maps)
+library(mapdata)
+library(leaflet)
+library(leaflet.extras)
+library(shinythemes)
+library(shiny)
+
+##################################################################
+# 2) Mortality-Analysis Functions
+##################################################################
+
+# -- Base function to fetch dead observations over a specified date range --
+fetch_dead_data_once <- function(
+    place_id    = NULL,
+    swlat       = NULL,
+    swlng       = NULL,
+    nelat       = NULL,
+    nelng       = NULL,
+    start_date,
+    end_date,
+    iconic_taxa = NULL,
+    taxon_name  = NULL,
+    conservation_status = NULL,
+    per_page    = 200,
+    max_pages   = 200
+) {
+  base_url <- "https://api.inaturalist.org/v1/observations"
+  
+  q_parts <- list(
+    "term_id=17",               # 'Dead' annotation
+    "term_value_id=19",         # 'Dead' annotation
+    "verifiable=true",          # only verifiable
+    glue("d1={start_date}"),    # start date
+    glue("d2={end_date}"),      # 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)}"))
+  }
+  
+  if (!is.null(conservation_status) && conservation_status != "") {
+    # If you'd like to filter by iNat conservation status,
+    # or e.g. pass additional parameters to the API
+    if (!grepl("=", conservation_status, fixed = TRUE)) {
+      q_parts <- c(q_parts, glue("cs={URLencode(conservation_status)}"))
+    } else {
+      q_parts <- c(q_parts, conservation_status)
+    }
+  }
+  
+  query_params <- paste(q_parts, collapse = "&")
+  
+  # Build location portion of query
+  loc_part <- ""
+  if (!is.null(place_id)) {
+    loc_part <- glue("&place_id={place_id}")
+  } else if (!is.null(swlat) && !is.null(swlng) &&
+             !is.null(nelat) && !is.null(nelng)) {
+    loc_part <- glue("&nelat={nelat}&nelng={nelng}&swlat={swlat}&swlng={swlng}")
+  } else {
+    stop("Must provide either 'place_id' OR bounding box (swlat, swlng, nelat, nelng).")
+  }
+  
+  observations_list <- list()
+  current_page <- 1
+  
+  while (current_page <= max_pages) {
+    query_url <- paste0(
+      base_url, "?", query_params, "&page=", current_page, loc_part
+    )
+    
+    message("Fetching page ", current_page,
+            " [", start_date, " to ", end_date, "]:\n", query_url)
+    
+    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$results) == 0) {
+      message("No more results at page ", current_page)
+      break
+    }
+    
+    obs_page_df <- as_tibble(parsed$results)
+    observations_list[[current_page]] <- obs_page_df
+    
+    # If the returned page is smaller than per_page, we've reached the last page
+    if (nrow(obs_page_df) < per_page) {
+      message("Reached last page of results at page ", current_page)
+      break
+    }
+    
+    current_page <- current_page + 1
+    Sys.sleep(1.4)  # Polite pause, reduced it from 1.5 initiallly
+  }
+  
+  observations_all <- bind_rows(observations_list)
+  return(observations_all)
+}
+
+# -- Function to fetch data by iterating through each WEEK of a given year --
+fetch_dead_data_weekly <- function(
+    year,
+    place_id    = NULL,
+    swlat       = NULL,
+    swlng       = NULL,
+    nelat       = NULL,
+    nelng       = NULL,
+    iconic_taxa = NULL,
+    taxon_name  = NULL,
+    conservation_status = NULL,
+    per_page    = 200,
+    max_pages   = 200
+) {
+  start_of_year <- as.Date(glue("{year}-01-01"))
+  end_of_year   <- as.Date(glue("{year}-12-31"))
+  
+  # Create a sequence of "week starts" from Jan 1 to Dec 31
+  week_starts <- seq.Date(start_of_year, end_of_year, by = "1 week")
+  
+  weekly_list <- list()
+  
+  for (i in seq_along(week_starts)) {
+    start_date <- week_starts[i]
+    # If not the last index, end_date = next start - 1 day, else clamp to year-end
+    if (i < length(week_starts)) {
+      end_date <- week_starts[i + 1] - 1
+    } else {
+      end_date <- end_of_year
+    }
+    
+    message("\n--- Querying ", year, ", Week #", i,
+            " [", start_date, " to ", end_date, "] ---")
+    
+    df_week <- fetch_dead_data_once(
+      place_id    = place_id,
+      swlat       = swlat,
+      swlng       = swlng,
+      nelat       = nelat,
+      nelng       = nelng,
+      start_date  = start_date,
+      end_date    = end_date,
+      iconic_taxa = iconic_taxa,
+      taxon_name  = taxon_name,
+      conservation_status = conservation_status,
+      per_page    = per_page,
+      max_pages   = max_pages
+    )
+    weekly_list[[i]] <- df_week
+    
+    Sys.sleep(1.5)
+  }
+  
+  year_df <- bind_rows(weekly_list)
+  return(year_df)
+}
+
+# -- Wrapper that iterates over multiple years, pulling data weekly for each year --
+getDeadVertebrates_weeklyLoop <- function(
+    years,                 # <--- No default: pass your own vector of years
+    place_id              = NULL,
+    swlat                 = NULL,
+    swlng                 = NULL,
+    nelat                 = NULL,
+    nelng                 = NULL,
+    iconic_taxa           = NULL,
+    taxon_name            = NULL,
+    conservation_status   = NULL,
+    per_page              = 500,
+    max_pages             = 500,
+    outdir                = NULL
+) {
+  all_years_list <- list()
+  
+  # For each year, run weekly fetch
+  for (yr in years) {
+    message("\n========= YEAR: ", yr, " ==========\n")
+    yr_df <- fetch_dead_data_weekly(
+      year       = yr,
+      place_id   = place_id,
+      swlat      = swlat,
+      swlng      = swlng,
+      nelat      = nelat,
+      nelng      = nelng,
+      iconic_taxa= iconic_taxa,
+      taxon_name = taxon_name,
+      conservation_status = conservation_status,
+      per_page   = per_page,
+      max_pages  = max_pages
+    ) %>%
+      mutate(Window = as.character(yr))
+    
+    all_years_list[[as.character(yr)]] <- yr_df
+  }
+  
+  merged_df_all <- bind_rows(all_years_list)
+  
+  # If no data found or missing crucial columns, create empty placeholders
+  if (!"created_at_details.date" %in% names(merged_df_all) ||
+      nrow(merged_df_all) == 0) {
+    daily_plot <- ggplot() +
+      labs(title = "No 'Dead' Observations Found", x = NULL, y = NULL) +
+      theme_void()
+    
+    wong_palette <- c(
+      "#000000","#CC6666","#D55E00","#E69F00",
+      "#0072B2", "#56B4E9",
+      "#009E73","#66CC99","#999933", "#F0E442",
+      "#CC79A7"
+    )
+    
+    top_species_plot <- ggplot() +
+      labs(title = "No species data", x = NULL, y = NULL) +
+      theme_void()
+    
+    map_hotspots_gg <- ggplot() +
+      labs(title = "No data for map") +
+      theme_void()
+    
+    return(list(
+      merged_df_all    = merged_df_all,
+      merged_df        = merged_df_all,
+      daily_plot       = daily_plot,
+      top_species_plot = top_species_plot,
+      map_hotspots_gg  = map_hotspots_gg,
+      daily_90th_quant = NA
+    ))
+  }
+  
+  # Optionally write out to disk
+  if (!is.null(outdir)) {
+    if (!dir.exists(outdir)) {
+      dir.create(outdir, recursive = TRUE)
+    }
+    readr::write_csv(merged_df_all, file.path(outdir, "merged_df_ALL_data.csv"))
+  }
+  
+  # Aggregate counts by day
+  counts_by_day <- merged_df_all %>%
+    mutate(obs_date = as.Date(`observed_on`)) %>%
+    group_by(Window, obs_date) %>%
+    summarise(n = n_distinct(id), .groups = "drop")
+  
+  y_max_value <- max(counts_by_day$n, na.rm = TRUE)
+  n_windows   <- length(unique(counts_by_day$Window))
+  wes_colors  <- wes_palette("Zissou1", n_windows, type = "discrete")
+  
+  # Daily line plot
+  
+  wong_palette <- c(
+    "#000000","#CC6666","#D55E00","#E69F00",
+    "#0072B2", "#56B4E9",
+    "#009E73","#66CC99","#999933", "#F0E442",
+    "#CC79A7"
+  )
+  
+  
+  
+  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", date_breaks = "1 month") +
+    scale_y_continuous(limits = c(0, y_max_value)) +
+    scale_color_manual(values = wong_palette) +
+    labs(
+      title = glue("Daily 'Dead' Observations (Years {paste(years, collapse=', ')})"),
+      x     = "Month",
+      y     = "Number of Observations",
+      color = "Year"
+    ) +
+    theme_minimal(base_size = 14) +
+    theme(axis.text.x = element_text(angle = 45, hjust = 1))
+  
+  # Top species bar plot
+  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$taxon.name)
+    
+    wong_palette <- c(
+      "#000000","#CC6666","#D55E00","#E69F00",
+      "#0072B2", "#56B4E9",
+      "#009E73","#66CC99","#999933", "#F0E442",
+      "#CC79A7"
+    )
+    
+    top_species_plot <- ggplot(species_top20, aes(
+      x   = reorder(taxon.name, -dead_count),
+      y   = dead_count,
+      fill= Window
+    )) +
+      geom_col(position = position_dodge(width = 0.7)) +
+      coord_flip() +
+      labs(
+        title = "Top 20 Species with 'Dead' Observations",
+        x     = "Species",
+        y     = "Number of Dead Observations",
+        fill  = "Year"
+      ) +
+      theme_minimal(base_size = 14)+
+      scale_fill_manual(values = wong_palette) 
+  } else {
+    top_species_plot <- ggplot() +
+      labs(title = "No 'taxon.name' column found", x = NULL, y = NULL) +
+      theme_void()
+  }
+  
+  # Identify "high mortality" days (>= 90th percentile)
+  daily_quantile <- quantile(counts_by_day$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 %>%
+    mutate(obs_date = as.Date(`observed_on`)) %>%
+    filter(obs_date %in% high_mortality_days)
+  
+  # --------------------------------------------------------------
+  # Hexbin Map of ALL data (replaces previous hotspot map section)
+  # --------------------------------------------------------------
+  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 {
+      min_lon <- min(location_df_all$longitude, na.rm = TRUE)
+      max_lon <- max(location_df_all$longitude, na.rm = TRUE)
+      min_lat <- min(location_df_all$latitude,  na.rm = TRUE)
+      max_lat <- max(location_df_all$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 = c(min_lon, max_lon),
+          ylim = c(min_lat, max_lat),
+          expand = TRUE
+        ) +
+        labs(
+          title = glue("'Dead' Wildlife Observations Hexbin Map (Years {paste(years, collapse=', ')})"),
+          x = "Longitude",
+          y = "Latitude"
+        ) +
+        theme_classic(base_size = 14) +
+        theme(
+          axis.text.x   = element_text(face = "bold", size = 16, color = 'black'),
+          axis.title.x  = element_text(face = "bold", size = 16, color = 'black'),
+          axis.text.y   = element_text(face = "bold", size = 16, color = 'black'),
+          axis.title.y  = element_text(face = "bold", size = 16, color = 'black')
+        )
+    }
+  } else {
+    map_hotspots_gg <- ggplot() +
+      labs(title = "No 'location' column for map") +
+      theme_void()
+  }
+  # --------------------------------------------------------------
+  
+  # Optionally save outputs
+  if (!is.null(outdir)) {
+    readr::write_csv(merged_high, file.path(outdir, "merged_df_top90.csv"))
+    ggsave(file.path(outdir, "daily_plot.png"),
+           daily_plot, width = 8, height = 5, dpi = 300)
+    ggsave(file.path(outdir, "top_species_plot.png"),
+           top_species_plot, width = 7, height = 7, dpi = 300)
+    ggsave(file.path(outdir, "hexbin_map.png"),
+           map_hotspots_gg, width = 8, height = 5, dpi = 300)
+  }
+  
+  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
+  ))
+}
+
+##################################################################
+# 3) Shiny App: UI + Server (Weekly Queries)
+##################################################################
+
+ui <- fluidPage(
+  theme = shinytheme("cosmo"),  # Use a professional theme from shinythemes
+  
+  # -- Logo and Title at the top --
+  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",
+        
+        # == Query Panel ==
+        tabPanel(
+          title = "Query",
+          br(),
+          radioButtons("region_mode", "Region Input Mode:",
+                       choices = c("Enter Numeric place_id"   = "place",
+                                   "Two-Click Bounding Box"    = "bbox"),
+                       selected = "bbox"),
+          
+          # If user chooses numeric "place_id"
+          conditionalPanel(
+            condition = "input.region_mode == 'place'",
+            numericInput("place_id",
+                         "Numeric place_id (e.g. 1 = USA, 6712 = Canada, 14 = California)",
+                         value = 1, min = 1, max = 999999, step = 1)
+          ),
+          
+          # If user chooses bounding box
+          conditionalPanel(
+            condition = "input.region_mode == 'bbox'",
+            helpText("Left-click once for the SW corner, once more for the NE corner."),
+            leafletOutput("map_two_click", height = "300px"),
+            br(),
+            actionButton("clear_bbox", "Clear bounding box"),
+            br(), br(),
+            verbatimTextOutput("bbox_coords")
+          ),
+          
+          # Years
+          checkboxGroupInput("years", "Select Year(s):",
+                             choices = 2018:2025,
+                             selected = c(2022, 2023)),
+          
+          # Query by iconic class or exact species
+          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(),
+          # Removed download of hotspot/top-90% CSV
+          downloadButton("downloadAll",   "Download ALL Data CSV", icon = icon("download"))
+        ),
+        
+        # == About Panel ==
+        tabPanel(
+          title = "About",
+          br(),
+          p("This Shiny application was created by Diego Ellis Soto (University of California Berkeley) in collabiration with Liam U. Taylor (Bowdoin University), Lizzy Edson (California Academy of Sciences), Christopher J. Schell (University of California Berkeley),Carl Boettiger (University of California Berkeley),Rebecca Johnsons (California Academy of Sciences).\n            It queries iNaturalist for observations that have been annotated as 'Dead' wildlife (term_id=17, term_value_id=19) in real time.\n            These data are updated daily on the iNaturalist API. The data is fetched via the iNaturalist API and summarized here designed for scientific or conservation purposes."),
+          p("Digital platforms of participatory science like iNaturalist allow everyday people to collect and share data about local biodiversity.\n            Recording observations of dead wildlife can help us track mortality events, disease spread, and other factors affecting animal populations.\n            In fact information on wildlife mortality are often more critical for conservation efforts than living ones."),
+          p("We encourage everyone to contribute their sightings responsibly, ensuring that any data on roadkill or other mortalities can help management and conservation efforts, and\n            raise public awareness.")
+          ),
+        # == Participatory Science Panel ==
+        # tabPanel(
+        #   title = "Participatory Science",
+        #   br(),
+        #   p("Digital platforms of participatory science like iNaturalist allow everyday people to collect and share data about local biodiversity.\n            Recording observations of dead wildlife can help us track mortality events, disease spread, and other factors affecting animal populations.\n            In fact information on wildlife mortality are often more critical for conservation efforts than living ones."),
+        #   p("We encourage everyone to contribute their sightings responsibly, ensuring that any data on roadkill or other mortalities can help management and conservation efforts, and\n            raise public awareness.")
+        # ),
+        # 
+        # == How To Use Panel ==
+        tabPanel(
+          title = "How to Use",
+          br(),
+          p("This application lets you retrieve data about dead wildlife observations from iNaturalist.\n            You can choose to manually provide a numeric place_id or define a custom bounding box by clicking twice on the map."),
+          p("You can also decide whether to query by taxon class (e.g. Aves) or by exact species name (e.g. Puma concolor)."),
+          p("After selecting your inputs, press 'Run Query.' and a CSV for downloads is provided: (1) for all data retrieved.")
+        )
+      )
+    ),
+    
+    mainPanel(
+      tabsetPanel(
+        tabPanel("Daily Time Series",    withSpinner(plotOutput("dailyPlot"), type = 6)),
+        tabPanel("Top Species",          withSpinner(plotOutput("speciesPlot"), type = 6)),
+        tabPanel("Hexbin Map (All Data)", withSpinner(plotOutput("hotspotMap"), type = 6)),
+        tabPanel("Data Table", withSpinner(DT::dataTableOutput("dataTable"), type = 6))
+      )
+    )
+  )
+)
+
+server <- function(input, output, session) {
+  
+  # Reactive values for bounding box corners
+  rv <- reactiveValues(
+    corner1 = NULL,
+    corner2 = NULL,
+    bbox    = NULL
+  )
+  
+  # Initialize map
+  output$map_two_click <- renderLeaflet({
+    leaflet() %>%
+      addTiles() %>%
+      setView(lng = -100, lat = 40, zoom = 4)
+  })
+  
+  # Handle bounding box clicks
+  observeEvent(input$map_two_click_click, {
+    req(input$region_mode == "bbox")
+    
+    click <- input$map_two_click_click
+    if (is.null(click)) return()
+    
+    lat_clicked <- click$lat
+    lng_clicked <- click$lng
+    
+    if (is.null(rv$corner1)) {
+      rv$corner1 <- c(lat_clicked, lng_clicked)
+      showNotification("First corner set. Now click for the opposite corner.")
+      
+      leafletProxy("map_two_click") %>%
+        clearMarkers() %>%
+        addMarkers(lng = lng_clicked, lat = lat_clicked, popup = "Corner 1")
+      
+      rv$corner2 <- NULL
+      rv$bbox    <- NULL
+      
+    } else {
+      rv$corner2 <- c(lat_clicked, lng_clicked)
+      
+      lat_min <- min(rv$corner1[1], rv$corner2[1])
+      lat_max <- max(rv$corner1[1], rv$corner2[1])
+      lng_min <- min(rv$corner1[2], rv$corner2[2])
+      lng_max <- max(rv$corner1[2], rv$corner2[2])
+      
+      rv$bbox <- c(lat_min, lng_min, lat_max, lng_max)
+      
+      showNotification("Second corner set. Bounding box defined!", duration = 2)
+      
+      leafletProxy("map_two_click") %>%
+        clearMarkers() %>%
+        addMarkers(lng = rv$corner1[2], lat = rv$corner1[1], popup = "Corner 1") %>%
+        addMarkers(lng = rv$corner2[2], lat = rv$corner2[1], popup = "Corner 2") %>%
+        clearShapes() %>%
+        addRectangles(
+          lng1 = lng_min, lat1 = lat_min,
+          lng2 = lng_max, lat2 = lat_max,
+          fillColor = "red", fillOpacity = 0.2,
+          color = "red"
+        )
+    }
+  })
+  
+  observeEvent(input$clear_bbox, {
+    rv$corner1 <- NULL
+    rv$corner2 <- NULL
+    rv$bbox    <- NULL
+    
+    leafletProxy("map_two_click") %>%
+      clearMarkers() %>%
+      clearShapes()
+  })
+  
+  output$bbox_coords <- renderText({
+    req(input$region_mode == "bbox")
+    
+    if (is.null(rv$bbox)) {
+      "No bounding box defined yet."
+    } else {
+      paste0(
+        "Bounding box:\n",
+        "SW corner: (", rv$bbox[1], ", ", rv$bbox[2], ")\n",
+        "NE corner: (", rv$bbox[3], ", ", rv$bbox[4], ")"
+      )
+    }
+  })
+  
+  # Store final query results
+  result_data <- reactiveVal(NULL)
+  
+  # Main "Run Query" button
+  observeEvent(input$run_query, {
+    req(input$years)
+    shiny::validate(need(length(input$years) > 0, "Please select at least one year."))
+    
+    yrs <- as.numeric(input$years)
+    
+    # Region logic
+    place_id_val <- NULL
+    swlat_val <- NULL
+    swlng_val <- NULL
+    nelat_val <- NULL
+    nelng_val <- NULL
+    
+    if (input$region_mode == "place") {
+      place_id_val <- input$place_id
+    } else {
+      shiny::validate(need(!is.null(rv$bbox), "Please click twice on the map to define bounding box."))
+      swlat_val <- rv$bbox[1]
+      swlng_val <- rv$bbox[2]
+      nelat_val <- rv$bbox[3]
+      nelng_val <- rv$bbox[4]
+    }
+    
+    # Query type logic
+    iconic_val <- NULL
+    species_val <- NULL
+    if (input$query_type == "iconic") {
+      iconic_val <- input$iconic_taxon
+    } else {
+      species_val <- input$species_name
+    }
+    
+    # Fetch data
+    withProgress(message = 'Fetching data from iNaturalist (Weekly)...', value = 0, {
+      incProgress(0.4)
+      
+      query_res <- getDeadVertebrates_weeklyLoop(
+        years        = yrs,
+        place_id     = place_id_val,
+        swlat        = swlat_val,
+        swlng        = swlng_val,
+        nelat        = nelat_val,
+        nelng        = nelng_val,
+        iconic_taxa  = iconic_val,
+        taxon_name   = species_val
+      )
+      
+      result_data(query_res)
+      incProgress(1)
+    })
+  })
+  
+  # Output plots
+  output$dailyPlot <- renderPlot({
+    req(result_data())
+    result_data()$daily_plot
+  })
+  
+  output$speciesPlot <- renderPlot({
+    req(result_data())
+    result_data()$top_species_plot
+  })
+  
+  output$hotspotMap <- renderPlot({
+    req(result_data())
+    result_data()$map_hotspots_gg
+  })
+  
+  # Output data table (top-90% subset)
+  output$dataTable <- DT::renderDataTable({
+    req(result_data())
+    # df <- result_data()$merged_df   # top 90% subset 
+    df <- result_data()$merged_df_all # all data 
+    
+    if (nrow(df) == 0) {
+      return(DT::datatable(
+        data.frame(Message = "No records found"),
+        options = list(pageLength = 20)
+      ))
+    }
+    
+    df <- df %>%
+      mutate(
+        inat_link = paste0(
+          "<a href='https://www.inaturalist.org/observations/",
+          id, "' target='_blank'>", id, "</a>"
+        )
+      )
+    
+    photo_col <- "taxon.default_photo.square_url"
+    if (photo_col %in% names(df)) {
+      df$image_thumb <- ifelse(
+        !is.na(df[[photo_col]]) & df[[photo_col]] != "",
+        paste0("<img src='", df[[photo_col]], "' width='50'/>"),
+        "No Img"
+      )
+    } else {
+      df$image_thumb <- "No Img"
+    }
+    
+    show_cols <- c(
+      "inat_link", "image_thumb", "taxon.name", "created_at_details.date",
+      setdiff(names(df), c("inat_link", "image_thumb", "taxon.name", "created_at_details.date"))
+    )
+    
+    DT::datatable(
+      df[, show_cols, drop = FALSE],
+      escape = FALSE,
+      options = list(pageLength = 20, autoWidth = TRUE)
+    )
+  })
+  
+  # Download handler for ALL data only (hotspot CSV button removed)
+  output$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)

poc/app_no90_dateslider_2025.R

@@ -0,0 +1,619 @@
+##################################################################
+# Single R Script: Mortality Analysis + Shiny – Hexbin Map (All Data)
+# Date‑range queries (no hard‑coded years)
+##################################################################
+
+### 1) Install/Load Required Packages ####
+required_packages <- c(
+  "httr", "jsonlite", "tidyverse", "glue", "lubridate",
+  "wesanderson", "viridis", "hexbin", "shinycssloaders",
+  "DT", "maps", "mapdata", "leaflet", "leaflet.extras",
+  "shinythemes", "shiny"
+)
+
+installed_packages <- rownames(installed.packages())
+for (pkg in required_packages) {
+  if (!pkg %in% installed_packages) {
+    install.packages(pkg, dependencies = TRUE)
+  }
+}
+
+library(httr)
+library(jsonlite)
+library(tidyverse)
+library(glue)
+library(lubridate)
+library(wesanderson)
+library(viridis)
+library(hexbin)
+library(shinycssloaders)
+library(DT)
+library(maps)
+library(mapdata)
+library(leaflet)
+library(leaflet.extras)
+library(shinythemes)
+library(shiny)
+
+##################################################################
+# 2) Mortality‑Analysis Functions
+##################################################################
+
+# -- Base function to fetch dead observations for a specific date span --
+fetch_dead_data_once <- function(
+    place_id    = NULL,
+    swlat       = NULL,
+    swlng       = NULL,
+    nelat       = NULL,
+    nelng       = NULL,
+    start_date,
+    end_date,
+    iconic_taxa = NULL,
+    taxon_name  = NULL,
+    conservation_status = NULL,
+    per_page    = 200,
+    max_pages   = 200
+) {
+  base_url <- "https://api.inaturalist.org/v1/observations"
+  
+  q_parts <- list(
+    "term_id=17",               # 'Dead' annotation
+    "term_value_id=19",         # 'Dead' annotation
+    "verifiable=true",          # only verifiable
+    glue("d1={start_date}"),    # start date
+    glue("d2={end_date}"),      # 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)}"))
+  }
+  if (!is.null(conservation_status) && conservation_status != "") {
+    if (!grepl("=", conservation_status, fixed = TRUE)) {
+      q_parts <- c(q_parts, glue("cs={URLencode(conservation_status)}"))
+    } else {
+      q_parts <- c(q_parts, conservation_status)
+    }
+  }
+  query_params <- paste(q_parts, collapse = "&")
+  
+  # Build location portion of query
+  loc_part <- ""
+  if (!is.null(place_id)) {
+    loc_part <- glue("&place_id={place_id}")
+  } else if (!is.null(swlat) && !is.null(swlng) &&
+             !is.null(nelat) && !is.null(nelng)) {
+    loc_part <- glue("&nelat={nelat}&nelng={nelng}&swlat={swlat}&swlng={swlng}")
+  } else {
+    stop("Must provide either 'place_id' OR bounding box (swlat, swlng, nelat, nelng).")
+  }
+  
+  observations_list <- list()
+  current_page <- 1
+  
+  while (current_page <= max_pages) {
+    query_url <- paste0(
+      base_url, "?", query_params, "&page=", current_page, loc_part
+    )
+    
+    message("Fetching page ", current_page,
+            " [", start_date, " to ", end_date, "]:\n", query_url)
+    
+    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$results) == 0) {
+      message("No more results at page ", current_page)
+      break
+    }
+    
+    obs_page_df <- as_tibble(parsed$results)
+    observations_list[[current_page]] <- obs_page_df
+    
+    # reached the last page?
+    if (nrow(obs_page_df) < per_page) {
+      message("Reached last page of results at page ", current_page)
+      break
+    }
+    
+    current_page <- current_page + 1
+    Sys.sleep(1.4)  # Polite pause
+  }
+  
+  observations_all <- bind_rows(observations_list)
+  return(observations_all)
+}
+
+# -- Fetch data weekly across an arbitrary date range --
+getDeadVertebrates_dateRange <- function(
+    start_date,            # Date object or string YYYY‑MM‑DD
+    end_date,              # Date object or string YYYY‑MM‑DD
+    place_id              = NULL,
+    swlat                 = NULL,
+    swlng                 = NULL,
+    nelat                 = NULL,
+    nelng                 = NULL,
+    iconic_taxa           = NULL,
+    taxon_name            = NULL,
+    conservation_status   = NULL,
+    per_page              = 500,
+    max_pages             = 500,
+    outdir                = NULL
+) {
+  # Ensure dates are Date objects
+  start_date <- as.Date(start_date)
+  end_date   <- as.Date(end_date)
+  if (start_date > end_date) {
+    stop("start_date must be earlier than 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
+    
+    message("\n--- Querying ", st, " to ", ed, " ---")
+    
+    df_week <- fetch_dead_data_once(
+      place_id    = place_id,
+      swlat       = swlat,
+      swlng       = swlng,
+      nelat       = nelat,
+      nelng       = nelng,
+      start_date  = st,
+      end_date    = ed,
+      iconic_taxa = iconic_taxa,
+      taxon_name  = taxon_name,
+      conservation_status = conservation_status,
+      per_page    = per_page,
+      max_pages   = max_pages
+    )
+    all_weeks_list[[i]] <- df_week
+    Sys.sleep(1.5)
+  }
+  
+  merged_df_all <- bind_rows(all_weeks_list)
+  
+  # If empty, return placeholders
+  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
+    ))
+  }
+  
+  # Add year column for plotting
+  merged_df_all <- merged_df_all %>%
+    mutate(obs_date = as.Date(observed_on),
+           Window   = format(obs_date, "%Y"))
+  
+  # Optionally write out
+  if (!is.null(outdir)) {
+    if (!dir.exists(outdir)) dir.create(outdir, recursive = TRUE)
+    readr::write_csv(merged_df_all, file.path(outdir, "merged_df_ALL_data.csv"))
+  }
+  
+  # Aggregate counts by day
+  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$n, na.rm = TRUE)
+  wes_colors  <- wes_palette("Zissou1", length(unique(counts_by_day$Window)), type = "discrete")
+  
+  wong_palette <- c(
+    "#000000", "#CC6666", "#D55E00", "#E69F00",
+    "#0072B2", "#56B4E9",
+    "#009E73", "#66CC99", "#999933", "#F0E442",
+    "#CC79A7"
+  )
+  
+  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)) +
+    scale_color_manual(values = wong_palette) +
+    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))
+  
+  # Top species plot
+  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$taxon.name)
+    
+    top_species_plot <- ggplot(species_top20, aes(
+      x   = reorder(taxon.name, -dead_count),
+      y   = dead_count,
+      fill= Window
+    )) +
+      geom_col(position = position_dodge(width = 0.7)) +
+      coord_flip() +
+      labs(
+        title = "Top 20 Species with 'Dead' Observations",
+        x     = "Species",
+        y     = "Number of Dead Observations",
+        fill  = "Year"
+      ) +
+      theme_minimal(base_size = 14) +
+      scale_fill_manual(values = wong_palette)
+  } else {
+    top_species_plot <- ggplot() +
+      labs(title = "No 'taxon.name' column found", x = NULL, y = NULL) +
+      theme_void()
+  }
+  
+  # Identify high‑mortality days (>= 90th percentile) – kept but no longer downloaded separately
+  daily_quantile <- quantile(counts_by_day$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)
+  
+  # Hexbin map for ALL data
+  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 {
+      # Calculate map limits from the data actually returned
+      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()
+  }
+      
+      
+  #   if (nrow(location_df_all) == 0) {
+  #     map_hotspots_gg <- ggplot() +
+  #       labs(title = "No spatial data available for map") +
+  #       theme_void()
+  #   } else {
+  #     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
+  #       ) +
+  #       coord_quickmap(xlim=bbox[c(1,3)], ylim=bbox[c(2,4)], expand=TRUE)+
+  #       scale_fill_viridis_c(option = "plasma", name = "Observation Count") +
+  #       coord_quickmap(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()
+  # }
+  
+  # Save optional outputs
+  if (!is.null(outdir)) {
+    readr::write_csv(merged_high, file.path(outdir, "merged_df_top90.csv"))
+    ggsave(file.path(outdir, "daily_plot.png"),       daily_plot,       width = 8, height = 5, dpi = 300)
+    ggsave(file.path(outdir, "top_species_plot.png"), top_species_plot, width = 7, height = 7, dpi = 300)
+    ggsave(file.path(outdir, "hexbin_map.png"),       map_hotspots_gg,  width = 8, height = 5, dpi = 300)
+  }
+  
+  return(list(
+    merged_df_all    = merged_df_all,
+    merged_df        = merged_high,  # kept for potential future use
+    daily_plot       = daily_plot,
+    top_species_plot = top_species_plot,
+    map_hotspots_gg  = map_hotspots_gg,
+    daily_90th_quant = daily_quantile
+  ))
+}
+
+##################################################################
+# 3) Shiny App: UI + Server
+##################################################################
+
+ui <- fluidPage(
+  theme = shinytheme("cosmo"),
+  
+  # -- Logo and Title --
+  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",
+                  
+                  # == Query Panel ==
+                  tabPanel("Query",
+                           br(),
+                           radioButtons("region_mode", "Region Input Mode:",
+                                        choices = c("Enter Numeric place_id" = "place",
+                                                    "Two‑Click Bounding Box"  = "bbox"),
+                                        selected = "bbox"),
+                           
+                           # place_id input
+                           conditionalPanel(
+                             condition = "input.region_mode == 'place'",
+                             numericInput("place_id", "Numeric place_id (e.g. 1 = USA, 14 = California)",
+                                          value = 1, min = 1, max = 999999, step = 1)
+                           ),
+                           
+                           # Bounding‑box selector
+                           conditionalPanel(
+                             condition = "input.region_mode == 'bbox'",
+                             helpText("Left‑click once for the SW corner, once more for the NE corner."),
+                             leafletOutput("map_two_click", height = "300px"),
+                             br(), actionButton("clear_bbox", "Clear bounding box"), br(), br(),
+                             verbatimTextOutput("bbox_coords")
+                           ),
+                           
+                           # Date‑range selector (replaces year toggle)
+                           dateRangeInput("date_range", "Select Date Range:",
+                                          start  = Sys.Date() - 365,
+                                          end    = Sys.Date(),
+                                          min    = "2010-01-01",
+                                          max    = Sys.Date()),
+                           
+                           # Query by iconic class or species
+                           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"))
+                  ),
+                  
+                  # == About Panel ==
+                  tabPanel("About",
+                           br(),
+                           p("This Shiny application was created by Diego Ellis‑Soto (UC Berkeley) with collaborators Liam U. Taylor (Bowdoin University), Lizzy Edson (California Academy of Sciences), Christopher J. Schell (UC Berkeley), Carl Boettiger (UC Berkeley), and Rebecca Johnson (California Academy of Sciences). It retrieves iNaturalist observations annotated as 'Dead' wildlife in real time for research and conservation analyses."),
+                           p("Participatory science platforms like iNaturalist empower community members to document biodiversity. Observations of dead wildlife help detect mortality events, disease spread, and other threats that can be critical for conservation."),
+                           p("Please contribute responsibly and ethically. Data on wildlife mortalities can inform management decisions and raise public awareness.")
+                  ),
+                  
+                  # == How to Use Panel ==
+                  tabPanel("How to Use",
+                           br(),
+                           p("1. Choose a region: enter a numeric place_id **or** define a custom bounding box by clicking twice on the map."),
+                           p("2. Pick a date range for your query. The app will fetch data week‑by‑week within that range."),
+                           p("3. Select either an iconic taxon class (e.g. Aves) **or** an exact species name."),
+                           p("4. Click **Run Query**. Visualisations and the full data table will update. You can download the complete dataset using the 'Download ALL Data CSV' button.")
+                  )
+      )
+    ),
+    
+    mainPanel(
+      tabsetPanel(
+        tabPanel("Daily Time Series",     withSpinner(plotOutput("dailyPlot"),   type = 6)),
+        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
+##################################################################
+
+server <- function(input, output, session) {
+  
+  # Reactive values for bounding box clicks
+  rv <- reactiveValues(corner1 = NULL, corner2 = NULL, bbox = NULL)
+  
+  # Initialise leaflet map
+  output$map_two_click <- renderLeaflet({
+    leaflet() %>% addTiles() %>% setView(lng = -100, lat = 40, zoom = 4)
+  })
+  
+  # Handle map clicks
+  observeEvent(input$map_two_click_click, {
+    req(input$region_mode == "bbox")
+    click <- input$map_two_click_click
+    if (is.null(click)) return()
+    
+    lat_clicked <- click$lat; lng_clicked <- click$lng
+    if (is.null(rv$corner1)) {
+      rv$corner1 <- c(lat_clicked, lng_clicked)
+      showNotification("First corner set. Now click for the opposite corner.")
+      leafletProxy("map_two_click") %>% clearMarkers() %>%
+        addMarkers(lng = lng_clicked, lat = lat_clicked, popup = "Corner 1")
+      rv$corner2 <- NULL; rv$bbox <- NULL
+    } else {
+      rv$corner2 <- c(lat_clicked, lng_clicked)
+      lat_min <- min(rv$corner1[1], rv$corner2[1]); lat_max <- max(rv$corner1[1], rv$corner2[1])
+      lng_min <- min(rv$corner1[2], rv$corner2[2]); lng_max <- max(rv$corner1[2], rv$corner2[2])
+      rv$bbox <- c(lat_min, lng_min, lat_max, lng_max)
+      
+      showNotification("Second corner set. Bounding box defined!", duration = 2)
+      
+      leafletProxy("map_two_click") %>% clearMarkers() %>%
+        addMarkers(lng = rv$corner1[2], lat = rv$corner1[1], popup = "Corner 1") %>%
+        addMarkers(lng = rv$corner2[2], lat = rv$corner2[1], popup = "Corner 2") %>%
+        clearShapes() %>%
+        addRectangles(lng1 = lng_min, lat1 = lat_min, lng2 = lng_max, lat2 = lat_max,
+                      fillColor = "red", fillOpacity = 0.2, color = "red")
+    }
+  })
+  
+  observeEvent(input$clear_bbox, {
+    rv$corner1 <- rv$corner2 <- rv$bbox <- NULL
+    leafletProxy("map_two_click") %>% clearMarkers() %>% clearShapes()
+  })
+  
+  output$bbox_coords <- renderText({
+    req(input$region_mode == "bbox")
+    if (is.null(rv$bbox)) "No bounding box defined yet." else paste0(
+      "Bounding box:\nSW: (", rv$bbox[1], ", ", rv$bbox[2], ")\nNE: (", rv$bbox[3], ", ", rv$bbox[4], ")")
+  })
+  
+  # Store query results
+  result_data <- reactiveVal(NULL)
+  
+  # Run query
+  observeEvent(input$run_query, {
+    req(input$date_range)
+    start_date <- as.Date(input$date_range[1])
+    end_date   <- as.Date(input$date_range[2])
+    
+    # Region params
+    place_id_val <- NULL; swlat_val <- NULL; swlng_val <- NULL; nelat_val <- NULL; nelng_val <- NULL
+    if (input$region_mode == "place") {
+      place_id_val <- input$place_id
+    } else {
+      validate(need(!is.null(rv$bbox), "Please define a bounding box by clicking twice on the map."))
+      swlat_val <- rv$bbox[1]; swlng_val <- rv$bbox[2]; nelat_val <- rv$bbox[3]; nelng_val <- rv$bbox[4]
+    }
+    
+    # Taxon params
+    iconic_val  <- if (input$query_type == "iconic") input$iconic_taxon  else NULL
+    species_val <- if (input$query_type == "species") input$species_name else NULL
+    
+    withProgress(message = 'Fetching data from iNaturalist (weekly)…', value = 0, {
+      incProgress(0.4)
+      query_res <- getDeadVertebrates_dateRange(
+        start_date    = start_date,
+        end_date      = end_date,
+        place_id      = place_id_val,
+        swlat         = swlat_val,
+        swlng         = swlng_val,
+        nelat         = nelat_val,
+        nelng         = nelng_val,
+        iconic_taxa   = iconic_val,
+        taxon_name    = species_val
+      )
+      result_data(query_res)
+      incProgress(1)
+    })
+  })
+  
+  # Render plots
+  output$dailyPlot   <- renderPlot({ req(result_data()); result_data()$daily_plot })
+  output$speciesPlot <- renderPlot({ req(result_data()); result_data()$top_species_plot })
+  output$hotspotMap  <- renderPlot({ req(result_data()); result_data()$map_hotspots_gg })
+  
+  # Data table (all data)
+  output$dataTable <- DT::renderDataTable({
+    req(result_data())
+    df <- result_data()$merged_df_all
+    if (nrow(df) == 0) {
+      return(DT::datatable(data.frame(Message = "No records found"), options = list(pageLength = 20)))
+    }
+    
+    df <- df %>% mutate(inat_link = paste0("<a href='https://www.inaturalist.org/observations/", id, "' target='_blank'>", id, "</a>"))
+    photo_col <- "taxon.default_photo.square_url"
+    if (photo_col %in% names(df)) {
+      df$image_thumb <- ifelse(!is.na(df[[photo_col]]) & df[[photo_col]] != "",
+                               paste0("<img src='", df[[photo_col]], "' width='50'/>"), "No Img")
+    } else {
+      df$image_thumb <- "No Img"
+    }
+    
+    show_cols <- c("inat_link", "image_thumb", "taxon.name", "created_at_details.date",
+                   setdiff(names(df), c("inat_link", "image_thumb", "taxon.name", "created_at_details.date")))
+    
+    DT::datatable(df[, show_cols, drop = FALSE], escape = FALSE,
+                  options = list(pageLength = 20, autoWidth = TRUE))
+  })
+  
+  # Download handler – ALL data only
+  output$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)

poc/app_no90_dateslider_progress_bar_2025.R

@@ -0,0 +1,595 @@
+##################################################################
+# Single R Script: Mortality Analysis + Shiny – Hexbin Map (All Data)
+# Date-range queries (no hard-coded years)
+##################################################################
+
+### 1) Install/Load Required Packages ####
+required_packages <- c(
+  "httr", "jsonlite", "tidyverse", "glue", "lubridate",
+  "wesanderson", "viridis", "hexbin", "shinycssloaders",
+  "DT", "maps", "mapdata", "leaflet", "leaflet.extras",
+  "shinythemes", "shiny"
+)
+
+installed_packages <- rownames(installed.packages())
+for (pkg in required_packages) {
+  if (!pkg %in% installed_packages) {
+    install.packages(pkg, dependencies = TRUE)
+  }
+}
+
+library(httr)
+library(jsonlite)
+library(tidyverse)
+library(glue)
+library(lubridate)
+library(wesanderson)
+library(viridis)
+library(hexbin)
+library(shinycssloaders)
+library(DT)
+library(maps)
+library(mapdata)
+library(leaflet)
+library(leaflet.extras)
+library(shinythemes)
+library(shiny)
+
+##################################################################
+# 2) Mortality-Analysis Functions
+##################################################################
+
+# -- Base function to fetch dead observations for a specific date span --
+fetch_dead_data_once <- function(
+    place_id    = NULL,
+    swlat       = NULL,
+    swlng       = NULL,
+    nelat       = NULL,
+    nelng       = NULL,
+    start_date,
+    end_date,
+    iconic_taxa = NULL,
+    taxon_name  = NULL,
+    conservation_status = NULL,
+    per_page    = 200,
+    max_pages   = 200
+) {
+  base_url <- "https://api.inaturalist.org/v1/observations"
+  
+  q_parts <- list(
+    "term_id=17",               # 'Dead' annotation
+    "term_value_id=19",         # 'Dead' annotation
+    "verifiable=true",          # only verifiable
+    glue("d1={start_date}"),    # start date
+    glue("d2={end_date}"),      # 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)}"))
+  }
+  if (!is.null(conservation_status) && conservation_status != "") {
+    if (!grepl("=", conservation_status, fixed = TRUE)) {
+      q_parts <- c(q_parts, glue("cs={URLencode(conservation_status)}"))
+    } else {
+      q_parts <- c(q_parts, conservation_status)
+    }
+  }
+  query_params <- paste(q_parts, collapse = "&")
+  
+  # Build location portion of query
+  loc_part <- ""
+  if (!is.null(place_id)) {
+    loc_part <- glue("&place_id={place_id}")
+  } else if (!is.null(swlat) && !is.null(swlng) &&
+             !is.null(nelat) && !is.null(nelng)) {
+    loc_part <- glue("&nelat={nelat}&nelng={nelng}&swlat={swlat}&swlng={swlng}")
+  } else {
+    stop("Must provide either 'place_id' OR bounding box (swlat, swlng, nelat, nelng).")
+  }
+  
+  observations_list <- list()
+  current_page <- 1
+  
+  while (current_page <= max_pages) {
+    query_url <- paste0(
+      base_url, "?", query_params, "&page=", current_page, loc_part
+    )
+    
+    message("Fetching page ", current_page,
+            " [", start_date, " to ", end_date, "]:\n", query_url)
+    
+    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$results) == 0) {
+      message("No more results at page ", current_page)
+      break
+    }
+    
+    obs_page_df <- as_tibble(parsed$results)
+    observations_list[[current_page]] <- obs_page_df
+    
+    # reached the last page?
+    if (nrow(obs_page_df) < per_page) {
+      message("Reached last page of results at page ", current_page)
+      break
+    }
+    
+    current_page <- current_page + 1
+    Sys.sleep(1.4)  # Polite pause
+  }
+  
+  observations_all <- bind_rows(observations_list)
+  return(observations_all)
+}
+
+# -- Fetch data weekly across an arbitrary date range --
+getDeadVertebrates_dateRange <- function(
+    start_date,            # Date object or string YYYY-MM-DD
+    end_date,              # Date object or string YYYY-MM-DD
+    place_id              = NULL,
+    swlat                 = NULL,
+    swlng                 = NULL,
+    nelat                 = NULL,
+    nelng                 = NULL,
+    iconic_taxa           = NULL,
+    taxon_name            = NULL,
+    conservation_status   = NULL,
+    per_page              = 500,
+    max_pages             = 500,
+    outdir                = NULL
+) {
+  # Ensure dates are Date objects
+  start_date <- as.Date(start_date)
+  end_date   <- as.Date(end_date)
+  if (start_date > end_date) {
+    stop("start_date must be earlier than 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
+    
+    message("\n--- Querying ", st, " to ", ed, " ---")
+    
+    # ── NEW: update Shiny progress bar ──────────────────────────────
+    try(
+      incProgress(
+        amount  = 1 / length(week_starts),
+        detail  = glue("Week {i} of {length(week_starts)}: {st} to {ed}")
+      ),
+      silent = TRUE
+    )
+    # ────────────────────────────────────────────────────────────────
+    
+    df_week <- fetch_dead_data_once(
+      place_id    = place_id,
+      swlat       = swlat,
+      swlng       = swlng,
+      nelat       = nelat,
+      nelng       = nelng,
+      start_date  = st,
+      end_date    = ed,
+      iconic_taxa = iconic_taxa,
+      taxon_name  = taxon_name,
+      conservation_status = conservation_status,
+      per_page    = per_page,
+      max_pages   = max_pages
+    )
+    all_weeks_list[[i]] <- df_week
+    Sys.sleep(1.4)
+  }
+  
+  merged_df_all <- bind_rows(all_weeks_list)
+  
+  # If empty, return placeholders
+  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
+    ))
+  }
+  
+  # Add year column for plotting
+  merged_df_all <- merged_df_all %>%
+    mutate(obs_date = as.Date(observed_on),
+           Window   = format(obs_date, "%Y"))
+  
+  # Optionally write out
+  if (!is.null(outdir)) {
+    if (!dir.exists(outdir)) dir.create(outdir, recursive = TRUE)
+    readr::write_csv(merged_df_all, file.path(outdir, "merged_df_ALL_data.csv"))
+  }
+  
+  # Aggregate counts by day
+  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$n, na.rm = TRUE)
+ #  wes_colors  <- wes_palette("Zissou1", length(unique(counts_by_day$Window)), type = "discrete")
+  
+  # wong_palette <- c(
+  #   "#000000", "#CC6666", "#D55E00", "#E69F00",
+  #   "#0072B2", "#56B4E9",
+  #   "#009E73", "#66CC99", "#999933", "#F0E442",
+  #   "#CC79A7"
+  # )
+  
+  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)) +
+    # scale_color_manual(values = wong_palette) +
+    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))
+  
+  # Top species plot
+  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$taxon.name)
+    
+    top_species_plot <- ggplot(species_top20, aes(
+      x   = reorder(taxon.name, -dead_count),
+      y   = dead_count,
+      fill= Window
+    )) +
+      geom_col(position = position_dodge(width = 0.7)) +
+      coord_flip() +
+      labs(
+        title = "Top 20 Species with 'Dead' Observations",
+        x     = "Species",
+        y     = "Number of Dead Observations",
+        fill  = "Year"
+      ) +
+      theme_minimal(base_size = 14)
+    #+
+     # scale_fill_manual(values = wong_palette)
+  } else {
+    top_species_plot <- ggplot() +
+      labs(title = "No 'taxon.name' column found", x = NULL, y = NULL) +
+      theme_void()
+  }
+  
+  # Identify high-mortality days (>= 90th percentile)
+  daily_quantile <- quantile(counts_by_day$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)
+  
+  # Hexbin map for ALL data
+  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 {
+      # Calculate map limits from the data actually returned
+      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, # play around with this
+          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()
+  }
+  
+  # Save optional outputs
+  if (!is.null(outdir)) {
+    readr::write_csv(merged_high, file.path(outdir, "merged_df_top90.csv"))
+    ggsave(file.path(outdir, "daily_plot.png"),       daily_plot,       width = 8, height = 5, dpi = 300)
+    ggsave(file.path(outdir, "top_species_plot.png"), top_species_plot, width = 7, height = 7, dpi = 300)
+    ggsave(file.path(outdir, "hexbin_map.png"),       map_hotspots_gg,  width = 8, height = 5, dpi = 300)
+  }
+  
+  return(list(
+    merged_df_all    = merged_df_all,
+    merged_df        = merged_high,  # kept for potential future use
+    daily_plot       = daily_plot,
+    top_species_plot = top_species_plot,
+    map_hotspots_gg  = map_hotspots_gg,
+    daily_90th_quant = daily_quantile
+  ))
+}
+
+##################################################################
+# 3) Shiny App: UI + Server
+##################################################################
+
+ui <- fluidPage(
+  theme = shinytheme("cosmo"),
+  
+  # -- Logo and Title --
+  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",
+                  
+                  # == Query Panel ==
+                  tabPanel("Query",
+                           br(),
+                           radioButtons("region_mode", "Region Input Mode:",
+                                        choices = c("Enter Numeric place_id" = "place",
+                                                    "Two-Click Bounding Box"  = "bbox"),
+                                        selected = "bbox"),
+                           
+                           # place_id input
+                           conditionalPanel(
+                             condition = "input.region_mode == 'place'",
+                             numericInput("place_id", "Numeric place_id (e.g. 1 = USA, 14 = California)",
+                                          value = 1, min = 1, max = 999999, step = 1)
+                           ),
+                           
+                           # Bounding-box selector
+                           conditionalPanel(
+                             condition = "input.region_mode == 'bbox'",
+                             helpText("Left-click once for the SW corner, once more for the NE corner."),
+                             leafletOutput("map_two_click", height = "300px"),
+                             br(), actionButton("clear_bbox", "Clear bounding box"), br(), br(),
+                             verbatimTextOutput("bbox_coords")
+                           ),
+                           
+                           # Date-range selector
+                           dateRangeInput("date_range", "Select Date Range:",
+                                          start  = Sys.Date() - 365,
+                                          end    = Sys.Date(),
+                                          min    = "2010-01-01",
+                                          max    = Sys.Date()),
+                           
+                           # Query by iconic class or species
+                           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"))
+                  ),
+                  
+                  # == About Panel ==
+                  tabPanel("About",
+                           br(),
+                           p("This Shiny application was created by Diego Ellis-Soto (UC Berkeley) with collaborators Liam U. Taylor (Bowdoin University), Lizzy Edson (California Academy of Sciences), Christopher J. Schell (UC Berkeley), Carl Boettiger (UC Berkeley), and Rebecca Johnson (California Academy of Sciences). It retrieves iNaturalist observations annotated as 'Dead' wildlife in real time for research and conservation analyses."),
+                           p("Participatory science platforms like iNaturalist empower community members to document biodiversity. Observations of dead wildlife help detect mortality events, disease spread, and other threats that can be critical for conservation."),
+                           p("Please contribute responsibly and ethically. Data on wildlife mortalities can inform management decisions and raise public awareness.")
+                  ),
+                  
+                  # == How to Use Panel ==
+                  tabPanel("How to Use",
+                           br(),
+                           p("1. Choose a region: enter a numeric place_id **or** define a custom bounding box by clicking twice on the map."),
+                           p("2. Pick a date range for your query. The app will fetch data week-by-week within that range."),
+                           p("3. Select either an iconic taxon class (e.g. Aves) **or** an exact species name."),
+                           p("4. Click **Run Query**. Visualisations and the full data table will update. You can download the complete dataset using the 'Download ALL Data CSV' button.")
+                  )
+      )
+    ),
+    
+    mainPanel(
+      tabsetPanel(
+        tabPanel("Daily Time Series",     withSpinner(plotOutput("dailyPlot"),   type = 6)),
+        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
+##################################################################
+
+server <- function(input, output, session) {
+  
+  # Reactive values for bounding box clicks
+  rv <- reactiveValues(corner1 = NULL, corner2 = NULL, bbox = NULL)
+  
+  # Initialise leaflet map
+  output$map_two_click <- renderLeaflet({
+    leaflet() %>% addTiles() %>% setView(lng = -100, lat = 40, zoom = 4)
+  })
+  
+  # Handle map clicks
+  observeEvent(input$map_two_click_click, {
+    req(input$region_mode == "bbox")
+    click <- input$map_two_click_click
+    if (is.null(click)) return()
+    
+    lat_clicked <- click$lat; lng_clicked <- click$lng
+    if (is.null(rv$corner1)) {
+      rv$corner1 <- c(lat_clicked, lng_clicked)
+      showNotification("First corner set. Now click for the opposite corner.")
+      leafletProxy("map_two_click") %>% clearMarkers() %>%
+        addMarkers(lng = lng_clicked, lat = lat_clicked, popup = "Corner 1")
+      rv$corner2 <- NULL; rv$bbox <- NULL
+    } else {
+      rv$corner2 <- c(lat_clicked, lng_clicked)
+      lat_min <- min(rv$corner1[1], rv$corner2[1]); lat_max <- max(rv$corner1[1], rv$corner2[1])
+      lng_min <- min(rv$corner1[2], rv$corner2[2]); lng_max <- max(rv$corner1[2], rv$corner2[2])
+      rv$bbox <- c(lat_min, lng_min, lat_max, lng_max)
+      
+      showNotification("Second corner set. Bounding box defined!", duration = 2)
+      
+      leafletProxy("map_two_click") %>% clearMarkers() %>%
+        addMarkers(lng = rv$corner1[2], lat = rv$corner1[1], popup = "Corner 1") %>%
+        addMarkers(lng = rv$corner2[2], lat = rv$corner2[1], popup = "Corner 2") %>%
+        clearShapes() %>%
+        addRectangles(lng1 = lng_min, lat1 = lat_min, lng2 = lng_max, lat2 = lat_max,
+                      fillColor = "red", fillOpacity = 0.2, color = "red")
+    }
+  })
+  
+  observeEvent(input$clear_bbox, {
+    rv$corner1 <- rv$corner2 <- rv$bbox <- NULL
+    leafletProxy("map_two_click") %>% clearMarkers() %>% clearShapes()
+  })
+  
+  output$bbox_coords <- renderText({
+    req(input$region_mode == "bbox")
+    if (is.null(rv$bbox)) "No bounding box defined yet." else paste0(
+      "Bounding box:\nSW: (", rv$bbox[1], ", ", rv$bbox[2], ")\nNE: (", rv$bbox[3], ", ", rv$bbox[4], ")")
+  })
+  
+  # Store query results
+  result_data <- reactiveVal(NULL)
+  
+  # Run query
+  observeEvent(input$run_query, {
+    req(input$date_range)
+    start_date <- as.Date(input$date_range[1])
+    end_date   <- as.Date(input$date_range[2])
+    
+    # Region params
+    place_id_val <- NULL; swlat_val <- NULL; swlng_val <- NULL; nelat_val <- NULL; nelng_val <- NULL
+    if (input$region_mode == "place") {
+      place_id_val <- input$place_id
+    } else {
+      validate(need(!is.null(rv$bbox), "Please define a bounding box by clicking twice on the map."))
+      swlat_val <- rv$bbox[1]; swlng_val <- rv$bbox[2]; nelat_val <- rv$bbox[3]; nelng_val <- rv$bbox[4]
+    }
+    
+    # Taxon params
+    iconic_val  <- if (input$query_type == "iconic") input$iconic_taxon  else NULL
+    species_val <- if (input$query_type == "species") input$species_name else NULL
+    
+    withProgress(message = 'Fetching data from iNaturalist…', value = 0, {
+      query_res <- getDeadVertebrates_dateRange(
+        start_date    = start_date,
+        end_date      = end_date,
+        place_id      = place_id_val,
+        swlat         = swlat_val,
+        swlng         = swlng_val,
+        nelat         = nelat_val,
+        nelng         = nelng_val,
+        iconic_taxa   = iconic_val,
+        taxon_name    = species_val
+      )
+      result_data(query_res)
+    })
+  })
+  
+  # Render plots
+  output$dailyPlot   <- renderPlot({ req(result_data()); result_data()$daily_plot })
+  output$speciesPlot <- renderPlot({ req(result_data()); result_data()$top_species_plot })
+  output$hotspotMap  <- renderPlot({ req(result_data()); result_data()$map_hotspots_gg })
+  
+  # Data table (all data)
+  output$dataTable <- DT::renderDataTable({
+    req(result_data())
+    df <- result_data()$merged_df_all
+    if (nrow(df) == 0) {
+      return(DT::datatable(data.frame(Message = "No records found"), options = list(pageLength = 20)))
+    }
+    
+    df <- df %>% mutate(inat_link = paste0("<a href='https://www.inaturalist.org/observations/", id, "' target='_blank'>", id, "</a>"))
+    photo_col <- "taxon.default_photo.square_url"
+    if (photo_col %in% names(df)) {
+      df$image_thumb <- ifelse(!is.na(df[[photo_col]]) & df[[photo_col]] != "",
+                               paste0("<img src='", df[[photo_col]], "' width='50'/>"), "No Img")
+    } else {
+      df$image_thumb <- "No Img"
+    }
+    
+    show_cols <- c("inat_link", "image_thumb", "taxon.name", "created_at_details.date",
+                   setdiff(names(df), c("inat_link", "image_thumb", "taxon.name", "created_at_details.date")))
+    
+    DT::datatable(df[, show_cols, drop = FALSE], escape = FALSE,
+                  options = list(pageLength = 20, autoWidth = TRUE))
+  })
+  
+  # Download handler – ALL data only
+  output$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)

poc/app_original_backup.R

@@ -0,0 +1,773 @@
+##################################################################
+# Single R Script: Mortality Analysis + Shiny - Two-Click BBox
+# Using Weekly Queries (No Hard-Coded Years)
+##################################################################
+
+# See https://www.inaturalist.org/pages/api+recommended+practices
+# Query Rate
+# Please keep requests to about 1 per second, and around 10k API requests a day
+# The API is meant to be used for building applications and for fetching small to medium batches of data. It is not meant to be a way to download data in bulk
+# Requests exceeding this limit might be throttled, and will return an HTTP 429 exception “Too Many Requests”
+# Please add delays into your code to keep under these limits, and especially if you’re getting 429 errors
+# We may block IPs that consistently exceed these limits
+# Please use a single IP address for fetching data. If we think multiple IPs are being used in coordination to bypass rate limits, we may block those IPs regardless of query rate
+# Downloading over 5 GB of media per hour or 24 GB of media per day may result in a permanent block
+# If writing software to interact with the API, please consider using a custom User Agent to identify your application, or iNaturalist username, or something we might use to differentiate your requests
+# The User Agent can be set with an HTTP header, e.g. User-Agent: [[application or user name]
+#
+
+### 1) Install/Load Required Packages ####
+required_packages <- c(
+  "httr", "jsonlite", "tidyverse", "glue", "lubridate",
+  "wesanderson", "viridis", "shinycssloaders",
+  "DT", "maps", "mapdata", "leaflet", "leaflet.extras",
+  "shinythemes", "shiny"
+)
+
+installed_packages <- rownames(installed.packages())
+for (pkg in required_packages) {
+  if (!pkg %in% installed_packages) {
+    install.packages(pkg, dependencies = TRUE)
+  }
+}
+
+library(httr)
+library(jsonlite)
+library(tidyverse)
+library(glue)
+library(lubridate)
+library(wesanderson)
+library(viridis)
+library(shinycssloaders)
+library(DT)
+library(maps)
+library(mapdata)
+library(leaflet)
+library(leaflet.extras)
+library(shinythemes)
+library(shiny)
+
+##################################################################
+# 2) Mortality-Analysis Functions
+##################################################################
+
+# -- Base function to fetch dead observations over a specified date range --
+fetch_dead_data_once <- function(
+    place_id    = NULL,
+    swlat       = NULL,
+    swlng       = NULL,
+    nelat       = NULL,
+    nelng       = NULL,
+    start_date,
+    end_date,
+    iconic_taxa = NULL,
+    taxon_name  = NULL,
+    conservation_status = NULL,
+    per_page    = 200,
+    max_pages   = 200
+) {
+  base_url <- "https://api.inaturalist.org/v1/observations"
+
+  q_parts <- list(
+    "term_id=17",               # 'Dead' annotation
+    "term_value_id=19",         # 'Dead' annotation
+    "verifiable=true",          # only verifiable
+    glue("d1={start_date}"),    # start date
+    glue("d2={end_date}"),      # 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)}"))
+  }
+
+  if (!is.null(conservation_status) && conservation_status != "") {
+    # If you'd like to filter by iNat conservation status,
+    # or e.g. pass additional parameters to the API
+    if (!grepl("=", conservation_status, fixed = TRUE)) {
+      q_parts <- c(q_parts, glue("cs={URLencode(conservation_status)}"))
+    } else {
+      q_parts <- c(q_parts, conservation_status)
+    }
+  }
+
+  query_params <- paste(q_parts, collapse = "&")
+
+  # Build location portion of query
+  loc_part <- ""
+  if (!is.null(place_id)) {
+    loc_part <- glue("&place_id={place_id}")
+  } else if (!is.null(swlat) && !is.null(swlng) &&
+             !is.null(nelat) && !is.null(nelng)) {
+    loc_part <- glue("&nelat={nelat}&nelng={nelng}&swlat={swlat}&swlng={swlng}")
+  } else {
+    stop("Must provide either 'place_id' OR bounding box (swlat, swlng, nelat, nelng).")
+  }
+
+  observations_list <- list()
+  current_page <- 1
+
+  while (current_page <= max_pages) {
+    query_url <- paste0(
+      base_url, "?", query_params, "&page=", current_page, loc_part
+    )
+
+    message("Fetching page ", current_page,
+            " [", start_date, " to ", end_date, "]:\n", query_url)
+
+    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$results) == 0) {
+      message("No more results at page ", current_page)
+      break
+    }
+
+    obs_page_df <- as_tibble(parsed$results)
+    observations_list[[current_page]] <- obs_page_df
+
+    # If the returned page is smaller than per_page, we've reached the last page
+    if (nrow(obs_page_df) < per_page) {
+      message("Reached last page of results at page ", current_page)
+      break
+    }
+
+    current_page <- current_page + 1
+    Sys.sleep(1.5)  # Polite pause
+  }
+
+  observations_all <- bind_rows(observations_list)
+  return(observations_all)
+}
+
+# -- Function to fetch data by iterating through each WEEK of a given year --
+fetch_dead_data_weekly <- function(
+    year,
+    place_id    = NULL,
+    swlat       = NULL,
+    swlng       = NULL,
+    nelat       = NULL,
+    nelng       = NULL,
+    iconic_taxa = NULL,
+    taxon_name  = NULL,
+    conservation_status = NULL,
+    per_page    = 200,
+    max_pages   = 200
+) {
+  start_of_year <- as.Date(glue("{year}-01-01"))
+  end_of_year   <- as.Date(glue("{year}-12-31"))
+
+  # Create a sequence of "week starts" from Jan 1 to Dec 31
+  week_starts <- seq.Date(start_of_year, end_of_year, by = "1 week")
+
+  weekly_list <- list()
+
+  for (i in seq_along(week_starts)) {
+    start_date <- week_starts[i]
+    # If not the last index, end_date = next start - 1 day, else clamp to year-end
+    if (i < length(week_starts)) {
+      end_date <- week_starts[i + 1] - 1
+    } else {
+      end_date <- end_of_year
+    }
+
+    message("\n--- Querying ", year, ", Week #", i,
+            " [", start_date, " to ", end_date, "] ---")
+
+    df_week <- fetch_dead_data_once(
+      place_id    = place_id,
+      swlat       = swlat,
+      swlng       = swlng,
+      nelat       = nelat,
+      nelng       = nelng,
+      start_date  = start_date,
+      end_date    = end_date,
+      iconic_taxa = iconic_taxa,
+      taxon_name  = taxon_name,
+      conservation_status = conservation_status,
+      per_page    = per_page,
+      max_pages   = max_pages
+    )
+    weekly_list[[i]] <- df_week
+
+    Sys.sleep(1.5)
+  }
+
+  year_df <- bind_rows(weekly_list)
+  return(year_df)
+}
+
+# -- Wrapper that iterates over multiple years, pulling data weekly for each year --
+getDeadVertebrates_weeklyLoop <- function(
+    years,                 # <--- No default: pass your own vector of years
+    place_id              = NULL,
+    swlat                 = NULL,
+    swlng                 = NULL,
+    nelat                 = NULL,
+    nelng                 = NULL,
+    iconic_taxa           = NULL,
+    taxon_name            = NULL,
+    conservation_status   = NULL,
+    per_page              = 500,
+    max_pages             = 500,
+    outdir                = NULL
+) {
+  all_years_list <- list()
+
+  # For each year, run weekly fetch
+  for (yr in years) {
+    message("\n========= YEAR: ", yr, " ==========\n")
+    yr_df <- fetch_dead_data_weekly(
+      year       = yr,
+      place_id   = place_id,
+      swlat      = swlat,
+      swlng      = swlng,
+      nelat      = nelat,
+      nelng      = nelng,
+      iconic_taxa= iconic_taxa,
+      taxon_name = taxon_name,
+      conservation_status = conservation_status,
+      per_page   = per_page,
+      max_pages  = max_pages
+    ) %>%
+      mutate(Window = as.character(yr))
+
+    all_years_list[[as.character(yr)]] <- yr_df
+  }
+
+  merged_df_all <- bind_rows(all_years_list)
+
+  # If no data found or missing crucial columns, create empty placeholders
+  if (!"created_at_details.date" %in% names(merged_df_all) ||
+      nrow(merged_df_all) == 0) {
+    daily_plot <- ggplot() +
+      labs(title = "No 'Dead' Observations Found", x = NULL, y = NULL) +
+      theme_void()
+
+    top_species_plot <- ggplot() +
+      labs(title = "No species data", x = NULL, y = NULL) +
+      theme_void()
+
+    map_hotspots_gg <- ggplot() +
+      labs(title = "No data for hotspots map") +
+      theme_void()
+
+    return(list(
+      merged_df_all    = merged_df_all,
+      merged_df        = merged_df_all,
+      daily_plot       = daily_plot,
+      top_species_plot = top_species_plot,
+      map_hotspots_gg  = map_hotspots_gg,
+      daily_90th_quant = NA
+    ))
+  }
+
+  # Optionally write out to disk
+  if (!is.null(outdir)) {
+    if (!dir.exists(outdir)) {
+      dir.create(outdir, recursive = TRUE)
+    }
+    readr::write_csv(merged_df_all, file.path(outdir, "merged_df_ALL_data.csv"))
+  }
+
+  # Aggregate counts by day
+  counts_by_day <- merged_df_all %>%
+    mutate(obs_date = as.Date(`observed_on`)) %>%
+    group_by(Window, obs_date) %>%
+    summarise(n = n_distinct(id), .groups = "drop")
+
+  y_max_value <- max(counts_by_day$n, na.rm = TRUE)
+   n_windows   <- length(unique(counts_by_day$Window))
+   wes_colors  <- wes_palette("Zissou1", n_windows, type = "discrete")
+
+  # Daily line plot
+  daily_plot <- ggplot(counts_by_day, aes(x = obs_date, y = n, color = Window)) +
+    geom_line(size = 1.2) +
+    geom_point(size = 2) +
+    # scale_color_viridis_d() +
+    scale_x_date(date_labels = "%b", date_breaks = "1 month") +
+    scale_y_continuous(limits = c(0, y_max_value)) +
+    labs(
+      title = glue("Daily 'Dead' Observations (Years {paste(years, collapse=', ')})"),
+      x     = "Month",
+      y     = "Number of Observations",
+      color = "Year"
+    ) +
+    theme_minimal(base_size = 14) +
+    theme(axis.text.x = element_text(angle = 45, hjust = 1))
+
+  # Top species bar plot
+  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$taxon.name)
+
+    top_species_plot <- ggplot(species_top20, aes(
+      x   = reorder(taxon.name, -dead_count),
+      y   = dead_count,
+      fill= Window
+    )) +
+      geom_col(position = position_dodge(width = 0.7)) +
+      coord_flip() +
+      # scale_fill_manual(values = wes_colors) +
+      # scale_color_viridis_d() +
+      labs(
+        title = "Top 20 Species with 'Dead' Observations",
+        x     = "Species",
+        y     = "Number of Dead Observations",
+        fill  = "Year"
+      ) +
+      theme_minimal(base_size = 14)
+  } else {
+    top_species_plot <- ggplot() +
+      labs(title = "No 'taxon.name' column found", x = NULL, y = NULL) +
+      theme_void()
+  }
+
+  # Identify "high mortality" days (>= 90th percentile)
+  daily_quantile <- quantile(counts_by_day$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 %>%
+    mutate(obs_date = as.Date(`observed_on`)) %>%
+    filter(obs_date %in% high_mortality_days)
+
+  # Map of top-90% mortality days
+  if ("location" %in% names(merged_high)) {
+    location_df <- merged_high %>%
+      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) == 0) {
+      map_hotspots_gg <- ggplot() +
+        labs(title = "No data in top 90th percentile days with valid location") +
+        theme_void()
+    } else {
+      min_lon <- min(location_df$longitude, na.rm = TRUE)
+      max_lon <- max(location_df$longitude, na.rm = TRUE)
+      min_lat <- min(location_df$latitude,  na.rm = TRUE)
+      max_lat <- max(location_df$latitude,  na.rm = TRUE)
+
+      map_hotspots_gg <- ggplot(location_df, aes(x = longitude, y = latitude, color = Window)) +
+        borders("world", fill = "gray80", colour = "white") +
+        geom_point(alpha = 0.6, size = 2) +
+        # scale_color_viridis_d() +
+        coord_quickmap(
+          xlim = c(min_lon, max_lon),
+          ylim = c(min_lat, max_lat),
+          expand = TRUE
+        ) +
+        labs(
+          title = glue("Top 90th percentile mortality days ({paste(years, collapse=', ')})"),
+          x     = "Longitude",
+          y     = "Latitude",
+          color = "Year"
+        ) +
+        theme_minimal(base_size = 14)
+    }
+  } else {
+    map_hotspots_gg <- ggplot() +
+      labs(title = "No 'location' column for top 90% days map") +
+      theme_void()
+  }
+
+  # Optionally save outputs
+  if (!is.null(outdir)) {
+    readr::write_csv(merged_high, file.path(outdir, "merged_df_top90.csv"))
+    ggsave(file.path(outdir, "daily_plot.png"),
+           daily_plot, width = 8, height = 5, dpi = 300)
+    ggsave(file.path(outdir, "top_species_plot.png"),
+           top_species_plot, width = 7, height = 7, dpi = 300)
+    ggsave(file.path(outdir, "map_hotspots.png"),
+           map_hotspots_gg, width = 8, height = 5, dpi = 300)
+  }
+
+  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
+  ))
+}
+
+##################################################################
+# 3) Shiny App: UI + Server (Weekly Queries)
+##################################################################
+
+ui <- fluidPage(
+  theme = shinytheme("cosmo"),  # Use a professional theme from shinythemes
+
+  # -- Logo and Title at the top --
+  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",
+
+        # == Query Panel ==
+        tabPanel(
+          title = "Query",
+          br(),
+          radioButtons("region_mode", "Region Input Mode:",
+                       choices = c("Enter Numeric place_id"   = "place",
+                                   "Two-Click Bounding Box"    = "bbox"),
+                       # choices = c(
+                       # "Two-Click Bounding Box"    = "bbox"),
+                       selected = "bbox"),
+
+          # If user chooses numeric "place_id"
+          conditionalPanel(
+            condition = "input.region_mode == 'place'",
+            numericInput("place_id",
+                         "Numeric place_id (e.g. 1 = USA, 6712 = Canada, 14 = California)",
+                         value = 1, min = 1, max = 999999, step = 1)
+          ),
+
+          # If user chooses bounding box
+          conditionalPanel(
+            condition = "input.region_mode == 'bbox'",
+            helpText("Left-click once for the SW corner, once more for the NE corner."),
+            leafletOutput("map_two_click", height = "300px"),
+            br(),
+            actionButton("clear_bbox", "Clear bounding box"),
+            br(), br(),
+            verbatimTextOutput("bbox_coords")
+          ),
+
+          # Years
+          checkboxGroupInput("years", "Select Year(s):",
+                             choices = 2018:2025,
+                             selected = c(2022, 2023)),
+
+          # Query by iconic class or exact species
+          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("downloadTop90", "Download Top-90% CSV", icon = icon("download")),
+          br(), br(),
+          downloadButton("downloadAll",   "Download ALL Data CSV", icon = icon("download"))
+        ),
+
+        # == About Panel ==
+        tabPanel(
+          title = "About",
+          br(),
+          p("This Shiny application was created by Diego Ellis Soto (University of California Berkeley).
+            It queries iNaturalist for observations that have been annotated as 'Dead' wildlife (term_id=17, term_value_id=19) in real time.
+            These data are updated daily on the iNaturalist API. The data is fetched via the iNaturalist API and summarized here designed for scientific or conservation purposes.")
+        ),
+        # == Participatory Science Panel ==
+        tabPanel(
+          title = "Participatory Science",
+          br(),
+          p("Digital platforms of participatory science like iNaturalist allow everyday people to collect and share data about local biodiversity.
+            Recording observations of dead wildlife can help us track mortality events, disease spread, and other factors affecting animal populations.
+            In fact information on wildlife mortality are often more critical for conservation efforts than living ones."),
+          p("We encourage everyone to contribute their sightings responsibly, ensuring that any data on roadkill or other mortalities can help management and conservation efforts, and
+            raise public awareness.")
+        ),
+
+        # == How To Use Panel ==
+        tabPanel(
+          title = "How to Use",
+          br(),
+          p("This application lets you retrieve data about dead wildlife observations from iNaturalist.
+            You can choose to manually provide a numeric place_id or define a custom bounding box by clicking twice on the map."),
+          p("You can also decide whether to query by taxon class (e.g. Aves) or by exact species name (e.g. Puma concolor)."),
+          # p("After selecting your inputs, press 'Run Query.' Two separate CSV downloads are provided: (1) for all data retrieved, and (2) for only the top-90% mortality days (for hotspot analysis).")
+          p("After selecting your inputs, press 'Run Query.' and a CSV for downloads is provided: (1) for all data retrieved.")
+        )
+      )
+    ),
+
+    mainPanel(
+      tabsetPanel(
+        tabPanel("Daily Time Series",    withSpinner(plotOutput("dailyPlot"), type = 6)),
+        tabPanel("Top Species",          withSpinner(plotOutput("speciesPlot"), type = 6)),
+        tabPanel("Hotspots Map (90th%)", withSpinner(plotOutput("hotspotMap"), type = 6)),
+        tabPanel("Data Table (Top-90%)", withSpinner(DT::dataTableOutput("dataTable"), type = 6))
+      )
+    )
+  )
+)
+
+server <- function(input, output, session) {
+
+  # Reactive values for bounding box corners
+  rv <- reactiveValues(
+    corner1 = NULL,
+    corner2 = NULL,
+    bbox    = NULL
+  )
+
+  # Initialize map
+  output$map_two_click <- renderLeaflet({
+    leaflet() %>%
+      addTiles() %>%
+      setView(lng = -100, lat = 40, zoom = 4)
+  })
+
+  # Handle bounding box clicks
+  observeEvent(input$map_two_click_click, {
+    req(input$region_mode == "bbox")
+
+    click <- input$map_two_click_click
+    if (is.null(click)) return()
+
+    lat_clicked <- click$lat
+    lng_clicked <- click$lng
+
+    if (is.null(rv$corner1)) {
+      rv$corner1 <- c(lat_clicked, lng_clicked)
+      showNotification("First corner set. Now click for the opposite corner.")
+
+      leafletProxy("map_two_click") %>%
+        clearMarkers() %>%
+        addMarkers(lng = lng_clicked, lat = lat_clicked, popup = "Corner 1")
+
+      rv$corner2 <- NULL
+      rv$bbox    <- NULL
+
+    } else {
+      rv$corner2 <- c(lat_clicked, lng_clicked)
+
+      lat_min <- min(rv$corner1[1], rv$corner2[1])
+      lat_max <- max(rv$corner1[1], rv$corner2[1])
+      lng_min <- min(rv$corner1[2], rv$corner2[2])
+      lng_max <- max(rv$corner1[2], rv$corner2[2])
+
+      rv$bbox <- c(lat_min, lng_min, lat_max, lng_max)
+
+      showNotification("Second corner set. Bounding box defined!", duration = 2)
+
+      leafletProxy("map_two_click") %>%
+        clearMarkers() %>%
+        addMarkers(lng = rv$corner1[2], lat = rv$corner1[1], popup = "Corner 1") %>%
+        addMarkers(lng = rv$corner2[2], lat = rv$corner2[1], popup = "Corner 2") %>%
+        clearShapes() %>%
+        addRectangles(
+          lng1 = lng_min, lat1 = lat_min,
+          lng2 = lng_max, lat2 = lat_max,
+          fillColor = "red", fillOpacity = 0.2,
+          color = "red"
+        )
+    }
+  })
+
+  observeEvent(input$clear_bbox, {
+    rv$corner1 <- NULL
+    rv$corner2 <- NULL
+    rv$bbox    <- NULL
+
+    leafletProxy("map_two_click") %>%
+      clearMarkers() %>%
+      clearShapes()
+  })
+
+  output$bbox_coords <- renderText({
+    req(input$region_mode == "bbox")
+
+    if (is.null(rv$bbox)) {
+      "No bounding box defined yet."
+    } else {
+      paste0(
+        "Bounding box:\n",
+        "SW corner: (", rv$bbox[1], ", ", rv$bbox[2], ")\n",
+        "NE corner: (", rv$bbox[3], ", ", rv$bbox[4], ")"
+      )
+    }
+  })
+
+  # Store final query results
+  result_data <- reactiveVal(NULL)
+
+  # Main "Run Query" button
+  observeEvent(input$run_query, {
+    req(input$years)
+    shiny::validate(need(length(input$years) > 0, "Please select at least one year."))
+
+    yrs <- as.numeric(input$years)
+
+    # Region logic
+    place_id_val <- NULL
+    swlat_val <- NULL
+    swlng_val <- NULL
+    nelat_val <- NULL
+    nelng_val <- NULL
+
+    if (input$region_mode == "place") {
+      place_id_val <- input$place_id
+    } else {
+      shiny::validate(need(!is.null(rv$bbox), "Please click twice on the map to define bounding box."))
+      swlat_val <- rv$bbox[1]
+      swlng_val <- rv$bbox[2]
+      nelat_val <- rv$bbox[3]
+      nelng_val <- rv$bbox[4]
+    }
+
+    # Query type logic
+    iconic_val <- NULL
+    species_val <- NULL
+    if (input$query_type == "iconic") {
+      iconic_val <- input$iconic_taxon
+    } else {
+      species_val <- input$species_name
+    }
+
+    # Fetch data
+    withProgress(message = 'Fetching data from iNaturalist (Weekly)...', value = 0, {
+      incProgress(0.4)
+
+      query_res <- getDeadVertebrates_weeklyLoop(
+        years        = yrs,
+        place_id     = place_id_val,
+        swlat        = swlat_val,
+        swlng        = swlng_val,
+        nelat        = nelat_val,
+        nelng        = nelng_val,
+        iconic_taxa  = iconic_val,
+        taxon_name   = species_val
+      )
+
+      result_data(query_res)
+      incProgress(1)
+    })
+  })
+
+  # Output plots
+  output$dailyPlot <- renderPlot({
+    req(result_data())
+    result_data()$daily_plot
+  })
+
+  output$speciesPlot <- renderPlot({
+    req(result_data())
+    result_data()$top_species_plot
+  })
+
+  output$hotspotMap <- renderPlot({
+    req(result_data())
+    result_data()$map_hotspots_gg
+  })
+
+  # Output data table (top-90% subset)
+  output$dataTable <- DT::renderDataTable({
+    req(result_data())
+    df <- result_data()$merged_df   # top 90% subset
+
+    if (nrow(df) == 0) {
+      return(DT::datatable(
+        data.frame(Message = "No records found"),
+        options = list(pageLength = 20) # Show 20 records
+      ))
+    }
+
+    df <- df %>%
+      mutate(
+        inat_link = paste0(
+          "<a href='https://www.inaturalist.org/observations/",
+          id, "' target='_blank'>", id, "</a>"
+        )
+      )
+
+    photo_col <- "taxon.default_photo.square_url"
+    if (photo_col %in% names(df)) {
+      df$image_thumb <- ifelse(
+        !is.na(df[[photo_col]]) & df[[photo_col]] != "",
+        paste0("<img src='", df[[photo_col]], "' width='50'/>"),
+        "No Img"
+      )
+    } else {
+      df$image_thumb <- "No Img"
+    }
+
+    show_cols <- c(
+      "inat_link", "image_thumb", "taxon.name", "created_at_details.date",
+      setdiff(names(df), c("inat_link", "image_thumb", "taxon.name", "created_at_details.date"))
+    )
+
+    DT::datatable(
+      df[, show_cols, drop = FALSE],
+      escape = FALSE,
+      options = list(pageLength = 20, autoWidth = TRUE) # Page 50 prior
+    )
+  })
+
+  # Download handlers
+  output$downloadTop90 <- downloadHandler(
+    filename = function() {
+      paste0("inat_dead_top90_", Sys.Date(), ".csv")
+    },
+    content = function(file) {
+      req(result_data())
+      readr::write_csv(result_data()$merged_df, file)
+    }
+  )
+
+  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)