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.gitattributes

@@ -32,3 +32,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+marine.rds filter=lfs diff=lfs merge=lfs -text

Dockerfile

@@ -0,0 +1,29 @@
+FROM rocker/r-base:latest
+
+# 设置工作目录
+WORKDIR /code
+
+# 安装系统依赖
+RUN apt-get update && apt-get install -y \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    libgdal-dev \
+    libgeos-dev \
+    libproj-dev \
+    libnetcdf-dev \
+    libudunits2-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# 安装 R 包
+RUN R -e "install.packages('shiny')" \
+    && R -e "install.packages('dplyr')" \
+    && R -e "install.packages('sf')" \
+    && R -e "install.packages('stringr')" \
+    && R -e "install.packages('leaflet')"
+
+# 复制应用代码
+COPY . .
+
+# 设置容器启动命令
+CMD ["R", "--quiet", "-e", "shiny::runApp(host='0.0.0.0', port=7860)"]

README.md

@@ -1,10 +1,10 @@
 ---
-title: Fishcas
+title: Fish Cas
 emoji: 🌍
 colorFrom: blue
-colorTo: blue
+colorTo: yellow
 sdk: docker
-pinned: true
+pinned: false
 license: apache-2.0
 short_description: Global fish distribution across biogeographic realm
 ---

app.R

@@ -0,0 +1,132 @@
+library(shiny)
+library(sf)
+library(stringr)
+library(dplyr)
+library(leaflet)
+
+options(sf_use_s2 = FALSE)
+
+# Load the shapefiles and data
+cas <- readRDS("cas.rds")
+
+inland <- readRDS("inland.rds")
+marine <- readRDS("marine.rds")
+
+
+# Example species list
+species_list <- sort(unique(cas$valid_name))
+
+
+ui <- fluidPage(
+  titlePanel("Global fish distribution across biogeographic realm"),
+  tags$head(tags$style(HTML("
+    body { background-color: #f2f2f2; color: #333333; }
+    .well { background-color: #ffffff; border: none; }
+    #map { height: 100vh; }  /* Set the map to take the full viewport height */
+    #controls {
+      background-color: rgba(255, 255, 255, 0.3);
+      padding: 15px;
+      border-radius: 8px;
+    }
+  "))),
+  fluidRow(
+    column(2,  # Left side navigation panel (20% of the width)
+           div(id = "controls", class = "panel panel-default",
+               fixed = FALSE, draggable = TRUE,
+               width = "100%", height = "100vh",
+               #img(src = "path_to_logo.png", height = "100px"), # Replace with actual logo path
+               selectizeInput("species",
+                              HTML(paste0("Choose/Input a species (<span style='color:red;'>", scales::comma(nrow(cas)), "</span>):")),
+                              choices = NULL,
+                              selected = NULL),
+               actionButton("run", "Run", class = "btn-primary")
+           ),
+           div(
+             tags$h5(HTML("<strong>Acknowledgements</strong>:")),
+             tags$p(HTML("<small>Heartfelt thanks to the hundreds of taxonomists for their selfless dedication. Data source (updated June 2024): <a href='http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp' target='_blank'> Eschmeyer's Catalog of Fishes</a>.</small>"))
+           ),
+           div(
+               tags$h5(HTML("<strong>References</strong>:")),
+               tags$p(HTML("<small>[1]Fricke R, Eschmeyer WN, Van der Laan R.(2024). <a href='http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp' ",
+                           "target='_blank'>Catalog of fishes: genera, species, references </a>. California Academy of Sciences, San Francisco, CA, USA.</small>")),
+               tags$p(HTML("<small>[2]Costello MJ, Tsai P, Wong PS, Cheung AKL, Basher Z, Chaudhary C.(2017). Marine biogeographic realms and species endemicity. <em>Nature Communications</em>, 8(1), 1057. </small>")),
+               tags$p(HTML("<small>[3]Tedesco PA, Beauchard O, Bigorne R, Blanchet S, Buisson L, Conti L, Cornu J,Dias MS, Grenouillet G, Hugueny B, Jézéquel C, Leprieur F, Brosse S, Oberdorff T.(2017). A global database on freshwater fish species occurrence in drainage basins. <em>Scientific Data</em>, 4(1), 1-6.</small>"))
+               ),
+           tags$map(HTML(paste0(
+             '<script type="text/javascript" id="clstr_globe" src="//clustrmaps.com/globe.js?d=fcrVhJisR3nagD85u6uUHpeDl2frZFCBy5i5BhDcpss"></script>'
+           ))),
+    ),
+    column(10,  # Right side map panel (80% of the width)
+           leafletOutput("map", width = "100%", height = "100vh")
+    )
+  )
+)
+
+
+# Server logic
+server <- function(input, output, session) {
+
+  # Update selectize input with species list (server-side)
+  updateSelectizeInput(session, "species",
+                       choices = species_list,
+                       server = TRUE)
+
+  observeEvent(input$run, {
+    sp <- input$species
+
+    realm <- cas %>%
+      dplyr::filter(valid_name %in% sp) %>%
+      dplyr::select(biogeographic_realm) %>%
+      str_split(";") %>%
+      unlist()
+
+
+    # Create map with Leaflet
+    output$map <- renderLeaflet({
+      leaflet() %>%
+        addProviderTiles("OpenStreetMap.Mapnik") %>%
+        addPolygons(data = marine[which(marine$name %in% realm),],
+                    fillColor = "#00A8E6", fillOpacity = 0.5, color = NA, group = "Marine") %>%
+        addPolygons(data = inland[which(inland$BasinName %in% realm),],
+                    fillColor = "#EEB134", fillOpacity = 0.5, color = NA, group = "Inland") %>%
+        #setView(lng = 0, lat = 20, zoom = 2) %>%
+        addControl(
+          html = paste(
+            "<strong>Data Source (Updated 2024-06): ",
+            "<a href='http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp' ",
+            "target='_blank'>Eschmeyer's Catalog of Fishes</a></strong><br>",
+            "<small>Feel free to contact: <a href='mailto:[email protected]'>[email protected]</a></small>"
+          ),
+          position = "bottomright",
+          className = "leaflet-control-custom"
+        )
+    })
+  })
+
+  # Add a popup showing species name and biogeographic realm on map click
+  observeEvent(input$map_click, {
+    click <- input$map_click
+    if (is.null(click))
+      return()
+
+    # Extract the species Latin name and realm for popup
+    sp <- input$species
+    habitat <- cas %>%
+      dplyr::filter(valid_name %in% sp) %>%
+      dplyr::select(habitat)
+
+    leafletProxy("map") %>%
+      clearPopups() %>%
+      addPopups(
+        lng = click$lng, lat = click$lat,
+        popup = paste0(
+          "<strong>Species: </strong>", "<em>", sp, "</em>",
+          "<br><strong>Habitat: </strong>", habitat
+        )
+      )
+  })
+
+}
+
+# Run the app
+shinyApp(ui, server)

marine.rds

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a170833dbc772067f0bb7a8adb72d3fbf14367861679e0950b6e533f4ae07fc5
+size 19635509