Now species specific query, full download

.ipynb_checkpoints/app-checkpoint.R

@@ -0,0 +1,672 @@
+##################################################################
+# Single R Script: Mortality Analysis + Shiny - Two-Click BBox
+##################################################################
+
+### 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
+##################################################################
+
+fetch_dead_data_once <- function(
+    place_id    = NULL,
+    swlat       = NULL,
+    swlng       = NULL,
+    nelat       = NULL,
+    nelng       = NULL,
+    start_date,
+    end_date,
+    iconic_taxa = "Aves",
+    per_page    = 1000,
+    max_pages   = 50
+) {
+  base_url <- "https://api.inaturalist.org/v1/observations"
+
+  query_params <- glue(
+    "iconic_taxa={iconic_taxa}&",
+    "term_id=17&",
+    "term_value_id=19&",
+    "verifiable=true&",
+    "d1={start_date}&d2={end_date}&",
+    "order=desc&order_by=created_at&",
+    "per_page={per_page}"
+  )
+
+  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 (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)  # polite pause for the API
+  }
+
+  observations_all <- bind_rows(observations_list)
+  return(observations_all)
+}
+
+
+fetch_dead_data_monthly <- function(
+    year,
+    place_id    = NULL,
+    swlat       = NULL,
+    swlng       = NULL,
+    nelat       = NULL,
+    nelng       = NULL,
+    iconic_taxa = "Aves"
+) {
+  monthly_list <- list()
+
+  for (month_i in 1:12) {
+    start_date <- as.Date(glue("{year}-{sprintf('%02d', month_i)}-01"))
+    end_date   <- start_date %m+% months(1) %m-% days(1)
+
+    if (year(start_date) != year) break
+
+    message("\n--- Querying ", year, ", month ", month_i, " ---")
+    df_month <- 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
+    )
+    monthly_list[[month_i]] <- df_month
+  }
+
+  year_df <- bind_rows(monthly_list)
+  return(year_df)
+}
+
+
+getDeadVertebrates_monthlyLoop <- function(
+    years       = c(2022, 2023),
+    place_id    = NULL,
+    swlat       = NULL,
+    swlng       = NULL,
+    nelat       = NULL,
+    nelng       = NULL,
+    iconic_taxa = "Aves",
+    per_page    = 1000,
+    max_pages   = 50,
+    outdir      = NULL
+) {
+  all_years_list <- list()
+  for (yr in years) {
+    message("\n========= YEAR: ", yr, " ==========\n")
+    yr_df <- fetch_dead_data_monthly(
+      year       = yr,
+      place_id   = place_id,
+      swlat      = swlat,
+      swlng      = swlng,
+      nelat      = nelat,
+      nelng      = nelng,
+      iconic_taxa= iconic_taxa
+    ) %>%
+      mutate(Window = as.character(yr))
+
+    all_years_list[[as.character(yr)]] <- yr_df
+  }
+
+  merged_df_all <- bind_rows(all_years_list)
+
+  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        = merged_df_all,
+      daily_plot       = daily_plot,
+      top_species_plot = top_species_plot,
+      map_hotspots_gg  = map_hotspots_gg
+    ))
+  }
+
+  if (!is.null(outdir)) {
+    if (!dir.exists(outdir)) {
+      dir.create(outdir, recursive = TRUE)
+    }
+    readr::write_csv(merged_df_all, file.path(outdir, "merged_df_top_all_data.csv"))
+  }
+
+  counts_by_day <- merged_df_all %>%
+    mutate(obs_date = as.Date(`created_at_details.date`)) %>%
+    group_by(Window, obs_date) %>%
+    summarise(n = n(), .groups = "drop")
+
+  n_windows  <- length(unique(counts_by_day$Window))
+  wes_colors <- wes_palette("Zissou1", n_windows, type = "discrete")
+
+  daily_plot <- ggplot(counts_by_day, aes(x = obs_date, y = n, color = Window)) +
+    geom_line(size = 1.2) +
+    geom_point(size = 2) +
+    scale_color_manual(values = wes_colors) +
+    scale_x_date(date_labels = "%b", date_breaks = "1 month") +
+    labs(
+      title = glue("Daily 'Dead' Observations (Years {paste(years, collapse=', ')})"),
+      x     = "Month",
+      y     = "Number of Observations",
+      color = "Year"
+    ) +
+    theme_minimal(base_size = 14) +
+    theme(axis.text.x = element_text(angle = 45, hjust = 1))
+
+  if ("taxon.name" %in% names(merged_df_all)) {
+    species_counts <- merged_df_all %>%
+      filter(!is.na(taxon.name)) %>%
+      group_by(Window, taxon.name) %>%
+      summarise(dead_count = n(), .groups = "drop")
+
+    top_species_overall <- species_counts %>%
+      group_by(taxon.name) %>%
+      summarise(total_dead = sum(dead_count)) %>%
+      arrange(desc(total_dead)) %>%
+      slice_head(n = 20)
+
+    species_top20 <- species_counts %>%
+      filter(taxon.name %in% top_species_overall$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) +
+      labs(
+        title = "Top 20 Species with 'Dead' Observations",
+        x     = "Species",
+        y     = "Number of Dead Observations",
+        fill  = "Year"
+      ) +
+      theme_minimal(base_size = 14)
+  } else {
+    top_species_plot <- ggplot() +
+      labs(title = "No 'taxon.name' column found", x = NULL, y = NULL) +
+      theme_void()
+  }
+
+  daily_quantile <- quantile(counts_by_day$n, probs = 0.90, na.rm = TRUE)
+  high_mortality_days <- counts_by_day %>%
+    filter(n >= daily_quantile) %>%
+    pull(obs_date)
+
+  merged_high <- merged_df_all %>%
+    mutate(obs_date = as.Date(`created_at_details.date`)) %>%
+    filter(obs_date %in% high_mortality_days)
+
+  if ("location" %in% names(merged_high)) {
+    location_df <- merged_high %>%
+      filter(!is.na(location) & location != "") %>%
+      separate(location, into = c("lat_str", "lon_str"), sep = ",", remove = FALSE) %>%
+      mutate(
+        latitude  = as.numeric(lat_str),
+        longitude = as.numeric(lon_str)
+      )
+
+    if (nrow(location_df) == 0) {
+      map_hotspots_gg <- ggplot() +
+        labs(title = "No data in top 90th percentile days with valid location") +
+        theme_void()
+    } else {
+      min_lon <- min(location_df$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$latitude,  na.rm = TRUE)
+
+      map_hotspots_gg <- ggplot(location_df, aes(x = longitude, y = latitude, color = Window)) +
+        borders("world", fill = "gray80", colour = "white") +
+        geom_point(alpha = 0.6, size = 2) +
+        scale_color_manual(values = wes_colors) +
+        coord_quickmap(xlim = c(min_lon, max_lon),
+                       ylim = c(min_lat, max_lat),
+                       expand = TRUE) +
+        labs(
+          title = glue("Top 90th percentile mortality days ({paste(years, collapse=', ')})"),
+          x     = "Longitude",
+          y     = "Latitude",
+          color = "Year"
+        ) +
+        theme_minimal(base_size = 14)
+    }
+  } else {
+    map_hotspots_gg <- ggplot() +
+      labs(title = "No 'location' column for top 90% days map") +
+      theme_void()
+  }
+
+  if (!is.null(outdir)) {
+    if (!dir.exists(outdir)) {
+      dir.create(outdir, recursive = TRUE)
+    }
+
+    readr::write_csv(merged_high, file.path(outdir, "merged_df_top90.csv"))
+    ggsave(file.path(outdir, "daily_plot.png"),
+           daily_plot, width = 8, height = 5, dpi = 300)
+    ggsave(file.path(outdir, "top_species_plot.png"),
+           top_species_plot, width = 7, height = 7, dpi = 300)
+    ggsave(file.path(outdir, "map_hotspots.png"),
+           map_hotspots_gg, width = 8, height = 5, dpi = 300)
+  }
+
+  return(list(
+    merged_df        = merged_high,
+    daily_plot       = daily_plot,
+    top_species_plot = top_species_plot,
+    map_hotspots_gg  = map_hotspots_gg,
+    daily_90th_quant = daily_quantile
+  ))
+}
+
+
+##################################################################
+# 3) Shiny App: UI + Server
+##################################################################
+
+ui <- fluidPage(
+  theme = shinytheme("flatly"),
+
+  # -- Logo and Title at the top --
+  fluidRow(
+    column(
+      width = 2,
+      # .all_logos.png in www folder
+      tags$img(src = "www/all_logos.png", height = "400px")
+    ),
+    column(
+      width = 10,
+      titlePanel("Dead Wildlife Observations from iNaturalist")
+    )
+  ),
+  hr(),
+
+  # Layout with a sidebar containing TABS: Query, About, Participatory, How to Use
+  sidebarLayout(
+    sidebarPanel(
+      tabsetPanel(
+        id = "sidebar_tabs",
+
+        # == Query Panel ==
+        tabPanel(
+          title = "Query",
+          br(),
+          radioButtons("query_mode", "Choose Query Mode:",
+                       choices = c("Use place_id" = "place",
+                                   "Two clicks to define bounding box" = "twoclick")),
+
+          # If place ID chosen, show numeric input
+          conditionalPanel(
+            condition = "input.query_mode == 'place'",
+            numericInput("place_id", "place_id (e.g. 1 for USA, 6712 for Canada)",
+                         value = 1, min = 1, max = 999999, step = 1)
+          ),
+
+          # If two-click BBox chosen, show Leaflet & bounding box info
+          conditionalPanel(
+            condition = "input.query_mode == 'twoclick'",
+            helpText("Left-click once for the first corner, and once more for the opposite corner.
+                      The SW and NE corners will be automatically computed."),
+            leafletOutput("map_two_click", height = "300px"),
+            br(),
+            actionButton("clear_bbox", "Clear bounding box"),
+            br(), br(),
+            verbatimTextOutput("bbox_coords")
+          ),
+
+          checkboxGroupInput("years", "Select Year(s):",
+                             choices = 2021:2025,
+                             selected = c(2021, 2022, 2023)),
+
+          selectInput("iconic_taxon", "Select Taxonomic Group:",
+                      choices = c("Aves", "Mammalia", "Reptilia", "Amphibia", "Actinopterygii", "Mollusca", "Animalia"),
+                      selected = "Aves"),
+
+          actionButton("run_query", "Run Query", icon = icon("play")),
+          hr(),
+          downloadButton("downloadData", "Download Top-90% 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 either specify a place_id (e.g., country or region) or define a custom bounding box with two clicks on the map.
+            After choosing which years and taxonomic group to query, press 'Run Query.'"),
+          p("These data are critical for understanding patterns of wildlife mortality, identifying hotspots of roadkill or disease, and informing conservation actions.
+            By systematically collecting and analyzing these records, conservation biologists and policymakers can make evidence-based decisions to protect wildlife populations.")
+        )
+      )
+    ),
+
+    # Main panel with tabbed outputs
+    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 to store bounding box corners from two clicks
+  rv <- reactiveValues(
+    corner1 = NULL,  # first click: (lat, lng)
+    corner2 = NULL,  # second click: (lat, lng)
+    bbox    = NULL   # computed bounding box: c(swlat, swlng, nelat, nelng)
+  )
+
+  # Render a simple Leaflet map (no draw toolbar).
+  output$map_two_click <- renderLeaflet({
+    leaflet() %>%
+      addTiles() %>%
+      setView(lng = -100, lat = 40, zoom = 4)
+  })
+
+  # Observe map clicks when "Two clicks to define bounding box" is selected
+  observeEvent(input$map_two_click_click, {
+    req(input$query_mode == "twoclick")
+
+    click <- input$map_two_click_click
+    if (is.null(click)) return()
+
+    lat_clicked <- click$lat
+    lng_clicked <- click$lng
+
+    # If corner1 is NULL, store the first corner
+    if (is.null(rv$corner1)) {
+      rv$corner1 <- c(lat_clicked, lng_clicked)
+      showNotification("First corner set. Now click for the opposite corner.")
+
+      # Add marker for the first corner
+      leafletProxy("map_two_click") %>%
+        clearMarkers() %>%  # remove any old markers
+        addMarkers(lng = lng_clicked, lat = lat_clicked,
+                   popup = "Corner 1")
+
+      rv$corner2 <- NULL
+      rv$bbox <- NULL
+
+    } else {
+      # This is the second corner
+      rv$corner2 <- c(lat_clicked, lng_clicked)
+
+      # We'll compute bounding box from the two corners
+      lat_min <- min(rv$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)
+
+      # Add marker for the second corner & a rectangle to visualize the bounding box
+      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") %>%
+        # draw rectangle
+        clearShapes() %>%
+        addRectangles(
+          lng1 = lng_min, lat1 = lat_min,
+          lng2 = lng_max, lat2 = lat_max,
+          fillColor = "red", fillOpacity = 0.2,
+          color = "red"
+        )
+    }
+  })
+
+  # Button to clear bounding box and reset corners
+  observeEvent(input$clear_bbox, {
+    rv$corner1 <- NULL
+    rv$corner2 <- NULL
+    rv$bbox    <- NULL
+
+    leafletProxy("map_two_click") %>%
+      clearMarkers() %>%
+      clearShapes()
+  })
+
+  # Show the user the bounding box
+  output$bbox_coords <- renderText({
+    req(input$query_mode == "twoclick")
+
+    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$bbox[4], ")"
+      )
+    }
+  })
+
+  # Reactive value to store final query results
+  result_data <- reactiveVal(NULL)
+
+  # "Run Query" button
+  observeEvent(input$run_query, {
+    req(input$years)
+    shiny::validate(shiny::need(length(input$years) > 0, "Please select at least one year"))
+
+    yrs <- as.numeric(input$years)
+
+    withProgress(message = 'Fetching data from iNaturalist...', value = 0, {
+      incProgress(0.3)
+
+      if (input$query_mode == "place") {
+        # place_id mode
+        place_id_val <- input$place_id
+        swlat_val <- NULL
+        swlng_val <- NULL
+        nelat_val <- NULL
+        nelng_val <- NULL
+
+      } else {
+        # two-click bounding box
+        shiny::validate(shiny::need(!is.null(rv$bbox), "Please click twice on the map to define bounding box."))
+
+        place_id_val <- NULL
+        swlat_val <- rv$bbox[1]
+        swlng_val <- rv$bbox[2]
+        nelat_val <- rv$bbox[3]
+        nelng_val <- rv$bbox[4]
+      }
+
+      query_res <- getDeadVertebrates_monthlyLoop(
+        years       = yrs,
+        place_id    = place_id_val,
+        swlat       = swlat_val,
+        swlng       = swlng_val,
+        nelat       = nelat_val,
+        nelng       = nelng_val,
+        iconic_taxa = input$iconic_taxon,
+        outdir      = NULL
+      )
+
+      result_data(query_res)
+      incProgress(1)
+    })
+  })
+
+  # (a) Daily Plot
+  output$dailyPlot <- renderPlot({
+    req(result_data())
+    result_data()$daily_plot
+  })
+
+  # (b) Top Species Plot
+  output$speciesPlot <- renderPlot({
+    req(result_data())
+    result_data()$top_species_plot
+  })
+
+  # (c) Hotspots Map
+  output$hotspotMap <- renderPlot({
+    req(result_data())
+    result_data()$map_hotspots_gg
+  })
+
+  # (d) Data Table (top-90% days)
+  output$dataTable <- DT::renderDataTable({
+    req(result_data())
+    df <- result_data()$merged_df
+
+    if (nrow(df) == 0) {
+      return(DT::datatable(data.frame(Message = "No records found"), options = list(pageLength = 5)))
+    }
+
+    df <- df %>%
+      mutate(
+        inat_link = paste0(
+          "<a href='https://www.inaturalist.org/observations/",
+          id, "' target='_blank'>", id, "</a>"
+        )
+      )
+
+    # If photos exist
+    photo_col <- "taxon.default_photo.square_url"
+    if (photo_col %in% names(df)) {
+      df$image_thumb <- ifelse(
+        !is.na(df[[photo_col]]) & df[[photo_col]] != "",
+        paste0("<img src='", df[[photo_col]], "' width='50'/>"),
+        "No Img"
+      )
+    } else {
+      df$image_thumb <- "No Img"
+    }
+
+    show_cols <- c(
+      "inat_link", "image_thumb", "taxon.name", "created_at_details.date",
+      setdiff(names(df), c("inat_link", "image_thumb", "taxon.name", "created_at_details.date"))
+    )
+
+    DT::datatable(
+      df[ , show_cols, drop = FALSE],
+      escape = FALSE,
+      options = list(pageLength = 10, autoWidth = TRUE)
+    )
+  })
+
+  # Download CSV handler
+  output$downloadData <- downloadHandler(
+    filename = function() {
+      paste0("inat_dead_top90_", Sys.Date(), ".csv")
+    },
+    content = function(file) {
+      req(result_data())
+      readr::write_csv(result_data()$merged_df, file)
+    }
+  )
+}
+
+# Run the Shiny app
+shinyApp(ui = ui, server = server)

app.R

@@ -7,7 +7,7 @@ required_packages <- c(
   "httr", "jsonlite", "tidyverse", "glue", "lubridate",
   "wesanderson", "viridis", "shinycssloaders",
   "DT", "maps", "mapdata", "leaflet", "leaflet.extras",
-  "shinythemes","shiny"
+  "shinythemes", "shiny"
 )
 
 installed_packages <- rownames(installed.packages())
@@ -21,6 +21,7 @@ library(httr)
 library(jsonlite)
 library(tidyverse)
 library(glue)
+require(viridis)
 library(lubridate)
 library(wesanderson)
 library(viridis)
@@ -33,7 +34,6 @@ library(leaflet.extras)
 library(shinythemes)
 library(shiny)
 
-
 ##################################################################
 # 2) Mortality-Analysis Functions
 ##################################################################
@@ -46,22 +46,45 @@ fetch_dead_data_once <- function(
     nelng       = NULL,
     start_date,
     end_date,
-    iconic_taxa = "Aves",
+    iconic_taxa = NULL,
+    taxon_name  = NULL,
+    # Removed conservation_status from UI, but function can still handle it if needed
+    conservation_status = NULL,
     per_page    = 1000,
     max_pages   = 50
 ) {
   base_url <- "https://api.inaturalist.org/v1/observations"
 
-  query_params <- glue(
-    "iconic_taxa={iconic_taxa}&",
-    "term_id=17&",
-    "term_value_id=19&",
-    "verifiable=true&",
-    "d1={start_date}&d2={end_date}&",
-    "order=desc&order_by=created_at&",
-    "per_page={per_page}"
+  q_parts <- list(
+    "term_id=17",
+    "term_value_id=19",
+    "verifiable=true",
+    glue("d1={start_date}"),
+    glue("d2={end_date}"),
+    "order=desc",
+    "order_by=created_at",
+    glue("per_page={per_page}")
   )
 
+  if (!is.null(iconic_taxa) && iconic_taxa != "") {
+    q_parts <- c(q_parts, glue("iconic_taxa={iconic_taxa}"))
+  }
+
+  if (!is.null(taxon_name) && taxon_name != "") {
+    q_parts <- c(q_parts, glue("taxon_name={URLencode(taxon_name)}"))
+  }
+
+  if (!is.null(conservation_status) && conservation_status != "") {
+    # The function remains flexible if you ever decide to pass a status again
+    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 = "&")
+
   loc_part <- ""
   if (!is.null(place_id)) {
     loc_part <- glue("&place_id={place_id}")
@@ -105,7 +128,7 @@ fetch_dead_data_once <- function(
     }
 
     current_page <- current_page + 1
-    Sys.sleep(1)  # polite pause for the API
+    Sys.sleep(1)  # polite pause
   }
 
   observations_all <- bind_rows(observations_list)
@@ -120,7 +143,8 @@ fetch_dead_data_monthly <- function(
     swlng       = NULL,
     nelat       = NULL,
     nelng       = NULL,
-    iconic_taxa = "Aves"
+    iconic_taxa = NULL,
+    taxon_name  = NULL
 ) {
   monthly_list <- list()
 
@@ -128,7 +152,7 @@ fetch_dead_data_monthly <- function(
     start_date <- as.Date(glue("{year}-{sprintf('%02d', month_i)}-01"))
     end_date   <- start_date %m+% months(1) %m-% days(1)
 
-    if (year(start_date) != year) break
+    if (lubridate::year(start_date) != year) break
 
     message("\n--- Querying ", year, ", month ", month_i, " ---")
     df_month <- fetch_dead_data_once(
@@ -139,7 +163,8 @@ fetch_dead_data_monthly <- function(
       nelng      = nelng,
       start_date = start_date,
       end_date   = end_date,
-      iconic_taxa= iconic_taxa
+      iconic_taxa= iconic_taxa,
+      taxon_name = taxon_name
     )
     monthly_list[[month_i]] <- df_month
   }
@@ -150,16 +175,19 @@ fetch_dead_data_monthly <- function(
 
 
 getDeadVertebrates_monthlyLoop <- function(
-    years       = c(2022, 2023),
-    place_id    = NULL,
-    swlat       = NULL,
-    swlng       = NULL,
-    nelat       = NULL,
-    nelng       = NULL,
-    iconic_taxa = "Aves",
-    per_page    = 1000,
-    max_pages   = 50,
-    outdir      = NULL
+    years                 = c(2022, 2023),
+    place_id              = NULL,
+    swlat                 = NULL,
+    swlng                 = NULL,
+    nelat                 = NULL,
+    nelng                 = NULL,
+    iconic_taxa           = NULL,
+    taxon_name            = NULL,
+    # Removed from UI, but function remains flexible
+    conservation_status   = NULL,
+    per_page              = 1000,
+    max_pages             = 50,
+    outdir                = NULL
 ) {
   all_years_list <- list()
   for (yr in years) {
@@ -171,7 +199,8 @@ getDeadVertebrates_monthlyLoop <- function(
       swlng      = swlng,
       nelat      = nelat,
       nelng      = nelng,
-      iconic_taxa= iconic_taxa
+      iconic_taxa= iconic_taxa,
+      taxon_name = taxon_name
     ) %>%
       mutate(Window = as.character(yr))
 
@@ -195,10 +224,12 @@ getDeadVertebrates_monthlyLoop <- function(
       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
+      map_hotspots_gg  = map_hotspots_gg,
+      daily_90th_quant = NA
     ))
   }
 
@@ -206,7 +237,7 @@ getDeadVertebrates_monthlyLoop <- function(
     if (!dir.exists(outdir)) {
       dir.create(outdir, recursive = TRUE)
     }
-    readr::write_csv(merged_df_all, file.path(outdir, "merged_df_top_all_data.csv"))
+    readr::write_csv(merged_df_all, file.path(outdir, "merged_df_ALL_data.csv"))
   }
 
   counts_by_day <- merged_df_all %>%
@@ -220,7 +251,7 @@ getDeadVertebrates_monthlyLoop <- function(
   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_manual(values = wes_colors) +
+    scale_color_viridis_d() +
     scale_x_date(date_labels = "%b", date_breaks = "1 month") +
     labs(
       title = glue("Daily 'Dead' Observations (Years {paste(years, collapse=', ')})"),
@@ -298,7 +329,7 @@ getDeadVertebrates_monthlyLoop <- function(
       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_manual(values = wes_colors) +
+        scale_color_viridis_d() +
         coord_quickmap(xlim = c(min_lon, max_lon),
                        ylim = c(min_lat, max_lat),
                        expand = TRUE) +
@@ -317,10 +348,6 @@ getDeadVertebrates_monthlyLoop <- function(
   }
 
   if (!is.null(outdir)) {
-    if (!dir.exists(outdir)) {
-      dir.create(outdir, recursive = TRUE)
-    }
-
     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)
@@ -331,6 +358,7 @@ getDeadVertebrates_monthlyLoop <- function(
   }
 
   return(list(
+    merged_df_all    = merged_df_all,
     merged_df        = merged_high,
     daily_plot       = daily_plot,
     top_species_plot = top_species_plot,
@@ -339,11 +367,41 @@ getDeadVertebrates_monthlyLoop <- function(
   ))
 }
 
-
 ##################################################################
 # 3) Shiny App: UI + Server
 ##################################################################
 
+# Example named vector of countries with known iNaturalist place_ids.
+# This is truncated. For a truly complete list, you may load from an external file
+# or build your own vector with place_ids from iNaturalist.
+country_choices <- c(
+  "Afghanistan" = 4337,
+  "Albania"     = 8563,
+  "Algeria"     = 9755,
+  "Andorra"     = 12244,
+  "Angola"      = 12242,
+  "Argentina"   = 28,
+  "Armenia"     = 8537,
+  "Australia"   = 6744,
+  "Austria"     = 8168,
+  "Bahamas"     = 7691,
+  "Bahrain"     = 11873,
+  "Bangladesh"  = 11884,
+  "Belarus"     = 8517,
+  "Belgium"     = 8034,
+  "Belize"      = 6881,
+  "Benin"       = 12345,
+  "Bhutan"      = 11905,
+  "Bolivia"     = 40,
+  "Bosnia and Herzegovina" = 8565,
+  "Botswana"    = 12271,
+  # ...
+  "United States" = 1,
+  "Canada"        = 6712,
+  "Mexico"        = 6883
+  # (Add more as needed)
+)
+
 ui <- fluidPage(
   theme = shinytheme("flatly"),
 
@@ -351,7 +409,6 @@ ui <- fluidPage(
   fluidRow(
     column(
       width = 2,
-      # .all_logos.png in www folder
       tags$img(src = "www/all_logos.png", height = "400px")
     ),
     column(
@@ -361,7 +418,6 @@ ui <- fluidPage(
   ),
   hr(),
 
-  # Layout with a sidebar containing TABS: Query, About, Participatory, How to Use
   sidebarLayout(
     sidebarPanel(
       tabsetPanel(
@@ -371,22 +427,31 @@ ui <- fluidPage(
         tabPanel(
           title = "Query",
           br(),
-          radioButtons("query_mode", "Choose Query Mode:",
-                       choices = c("Use place_id" = "place",
-                                   "Two clicks to define bounding box" = "twoclick")),
+          # 1) Radio to pick how to define region
+          radioButtons("region_mode", "Region Input Mode:",
+                       choices = c("Select Country by Name" = "country",
+                                   "Enter Numeric place_id"   = "place",
+                                   "Two-Click Bounding Box"    = "bbox")),
+
+          # All countries from a large list
+          conditionalPanel(
+            condition = "input.region_mode == 'country'",
+            selectInput("country_selection", "Select Country:",
+                        choices = country_choices,
+                        selected = 6712)  # e.g., Canada by default
+          ),
 
-          # If place ID chosen, show numeric input
+          # Manually typed place_id
           conditionalPanel(
-            condition = "input.query_mode == 'place'",
-            numericInput("place_id", "place_id (e.g. 1 for USA, 6712 for Canada)",
+            condition = "input.region_mode == 'place'",
+            numericInput("place_id", "Numeric place_id (e.g. 1 = USA, 6712 = Canada)",
                          value = 1, min = 1, max = 999999, step = 1)
           ),
 
-          # If two-click BBox chosen, show Leaflet & bounding box info
+          # Two-click bounding box
           conditionalPanel(
-            condition = "input.query_mode == 'twoclick'",
-            helpText("Left-click once for the first corner, and once more for the opposite corner.
-                      The SW and NE corners will be automatically computed."),
+            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"),
@@ -394,17 +459,37 @@ ui <- fluidPage(
             verbatimTextOutput("bbox_coords")
           ),
 
+          # Years
           checkboxGroupInput("years", "Select Year(s):",
-                             choices = 2021:2025,
-                             selected = c(2021, 2022, 2023)),
+                             choices = 2018:2025,
+                             selected = c(2022, 2023)),
+
+          # 2) Radio: either 'Taxon Class' or exact species name
+          radioButtons("query_type", "Query By:",
+                       choices = c("Taxon Class" = "iconic",
+                                   "Exact Species Name" = "species")),
+          # If 'Taxon Class' is chosen:
+          conditionalPanel(
+            condition = "input.query_type == 'iconic'",
+            selectInput("iconic_taxon", "Select Taxon Class:",
+                        choices = c("Aves", "Mammalia", "Reptilia", "Amphibia",
+                                    "Actinopterygii", "Mollusca", "Animalia"),
+                        selected = "Aves")
+          ),
+          # If species name is chosen:
+          conditionalPanel(
+            condition = "input.query_type == 'species'",
+            textInput("species_name", "Enter exact species name (e.g. Puma concolor)", "")
+          ),
 
-          selectInput("iconic_taxon", "Select Taxonomic Group:",
-                      choices = c("Aves", "Mammalia", "Reptilia", "Amphibia", "Actinopterygii", "Mollusca", "Animalia"),
-                      selected = "Aves"),
+          # Removed the Conservation Status input
 
           actionButton("run_query", "Run Query", icon = icon("play")),
           hr(),
-          downloadButton("downloadData", "Download Top-90% CSV", icon = icon("download"))
+          # Two Download buttons: top 90% vs. ALL data
+          downloadButton("downloadTop90", "Download Top-90% CSV", icon = icon("download")),
+          br(), br(),
+          downloadButton("downloadAll",   "Download ALL Data CSV",  icon = icon("download"))
         ),
 
         # == About Panel ==
@@ -431,10 +516,9 @@ ui <- fluidPage(
           title = "How to Use",
           br(),
           p("This application lets you retrieve data about dead wildlife observations from iNaturalist.
-            You can either specify a place_id (e.g., country or region) or define a custom bounding box with two clicks on the map.
-            After choosing which years and taxonomic group to query, press 'Run Query.'"),
-          p("These data are critical for understanding patterns of wildlife mortality, identifying hotspots of roadkill or disease, and informing conservation actions.
-            By systematically collecting and analyzing these records, conservation biologists and policymakers can make evidence-based decisions to protect wildlife populations.")
+            You can choose a country name, 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).")
         )
       )
     ),
@@ -453,23 +537,20 @@ ui <- fluidPage(
 
 server <- function(input, output, session) {
 
-  # Reactive values to store bounding box corners from two clicks
   rv <- reactiveValues(
-    corner1 = NULL,  # first click: (lat, lng)
-    corner2 = NULL,  # second click: (lat, lng)
-    bbox    = NULL   # computed bounding box: c(swlat, swlng, nelat, nelng)
+    corner1 = NULL,
+    corner2 = NULL,
+    bbox    = NULL
   )
 
-  # Render a simple Leaflet map (no draw toolbar).
   output$map_two_click <- renderLeaflet({
     leaflet() %>%
       addTiles() %>%
       setView(lng = -100, lat = 40, zoom = 4)
   })
 
-  # Observe map clicks when "Two clicks to define bounding box" is selected
   observeEvent(input$map_two_click_click, {
-    req(input$query_mode == "twoclick")
+    req(input$region_mode == "bbox")
 
     click <- input$map_two_click_click
     if (is.null(click)) return()
@@ -477,25 +558,20 @@ server <- function(input, output, session) {
     lat_clicked <- click$lat
     lng_clicked <- click$lng
 
-    # If corner1 is NULL, store the first corner
     if (is.null(rv$corner1)) {
       rv$corner1 <- c(lat_clicked, lng_clicked)
       showNotification("First corner set. Now click for the opposite corner.")
 
-      # Add marker for the first corner
       leafletProxy("map_two_click") %>%
-        clearMarkers() %>%  # remove any old markers
-        addMarkers(lng = lng_clicked, lat = lat_clicked,
-                   popup = "Corner 1")
+        clearMarkers() %>%
+        addMarkers(lng = lng_clicked, lat = lat_clicked, popup = "Corner 1")
 
       rv$corner2 <- NULL
-      rv$bbox <- NULL
+      rv$bbox    <- NULL
 
     } else {
-      # This is the second corner
       rv$corner2 <- c(lat_clicked, lng_clicked)
 
-      # We'll compute bounding box from the two corners
       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])
@@ -505,14 +581,10 @@ server <- function(input, output, session) {
 
       showNotification("Second corner set. Bounding box defined!", duration = 2)
 
-      # Add marker for the second corner & a rectangle to visualize the bounding box
       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") %>%
-        # draw rectangle
+        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,
@@ -523,7 +595,6 @@ server <- function(input, output, session) {
     }
   })
 
-  # Button to clear bounding box and reset corners
   observeEvent(input$clear_bbox, {
     rv$corner1 <- NULL
     rv$corner2 <- NULL
@@ -534,9 +605,8 @@ server <- function(input, output, session) {
       clearShapes()
   })
 
-  # Show the user the bounding box
   output$bbox_coords <- renderText({
-    req(input$query_mode == "twoclick")
+    req(input$region_mode == "bbox")
 
     if (is.null(rv$bbox)) {
       "No bounding box defined yet."
@@ -549,38 +619,45 @@ server <- function(input, output, session) {
     }
   })
 
-  # Reactive value to store final query results
   result_data <- reactiveVal(NULL)
 
-  # "Run Query" button
   observeEvent(input$run_query, {
     req(input$years)
-    shiny::validate(shiny::need(length(input$years) > 0, "Please select at least one year"))
+    shiny::validate(shiny::need(length(input$years) > 0, "Please select at least one year."))
 
     yrs <- as.numeric(input$years)
 
+    place_id_val <- NULL
+    swlat_val <- NULL
+    swlng_val <- NULL
+    nelat_val <- NULL
+    nelng_val <- NULL
+
+    if (input$region_mode == "country") {
+      place_id_val <- as.numeric(input$country_selection)
+
+    } else if (input$region_mode == "place") {
+      place_id_val <- input$place_id
+
+    } else {
+      shiny::validate(shiny::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$bbox[4]
+    }
+
+    iconic_val <- NULL
+    species_val <- NULL
+    if (input$query_type == "iconic") {
+      iconic_val <- input$iconic_taxon
+    } else {
+      species_val <- input$species_name
+    }
+
     withProgress(message = 'Fetching data from iNaturalist...', value = 0, {
       incProgress(0.3)
 
-      if (input$query_mode == "place") {
-        # place_id mode
-        place_id_val <- input$place_id
-        swlat_val <- NULL
-        swlng_val <- NULL
-        nelat_val <- NULL
-        nelng_val <- NULL
-
-      } else {
-        # two-click bounding box
-        shiny::validate(shiny::need(!is.null(rv$bbox), "Please click twice on the map to define bounding box."))
-
-        place_id_val <- NULL
-        swlat_val <- rv$bbox[1]
-        swlng_val <- rv$bbox[2]
-        nelat_val <- rv$bbox[3]
-        nelng_val <- rv$bbox[4]
-      }
-
       query_res <- getDeadVertebrates_monthlyLoop(
         years       = yrs,
         place_id    = place_id_val,
@@ -588,8 +665,9 @@ server <- function(input, output, session) {
         swlng       = swlng_val,
         nelat       = nelat_val,
         nelng       = nelng_val,
-        iconic_taxa = input$iconic_taxon,
-        outdir      = NULL
+        iconic_taxa = iconic_val,
+        taxon_name  = species_val
+        # Removed conservation_status from the call
       )
 
       result_data(query_res)
@@ -597,31 +675,28 @@ server <- function(input, output, session) {
     })
   })
 
-  # (a) Daily Plot
   output$dailyPlot <- renderPlot({
     req(result_data())
     result_data()$daily_plot
   })
 
-  # (b) Top Species Plot
   output$speciesPlot <- renderPlot({
     req(result_data())
     result_data()$top_species_plot
   })
 
-  # (c) Hotspots Map
   output$hotspotMap <- renderPlot({
     req(result_data())
     result_data()$map_hotspots_gg
   })
 
-  # (d) Data Table (top-90% days)
   output$dataTable <- DT::renderDataTable({
     req(result_data())
-    df <- result_data()$merged_df
+    df <- result_data()$merged_df   # top 90% subset
 
     if (nrow(df) == 0) {
-      return(DT::datatable(data.frame(Message = "No records found"), options = list(pageLength = 5)))
+      return(DT::datatable(data.frame(Message = "No records found"),
+                           options = list(pageLength = 5)))
     }
 
     df <- df %>%
@@ -632,7 +707,6 @@ server <- function(input, output, session) {
         )
       )
 
-    # If photos exist
     photo_col <- "taxon.default_photo.square_url"
     if (photo_col %in% names(df)) {
       df$image_thumb <- ifelse(
@@ -656,8 +730,7 @@ server <- function(input, output, session) {
     )
   })
 
-  # Download CSV handler
-  output$downloadData <- downloadHandler(
+  output$downloadTop90 <- downloadHandler(
     filename = function() {
       paste0("inat_dead_top90_", Sys.Date(), ".csv")
     },
@@ -666,7 +739,16 @@ server <- function(input, output, session) {
       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)
+    }
+  )
 }
 
-# Run the Shiny app
 shinyApp(ui = ui, server = server)