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app.R
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## --------------------------------------------------------------------------------------##
##
## Script name: app.R
##
## Purpose of the script:
##
## @author: Chinmay Deval
##
## Created on Fri Sept 04 19:35:48 2020
##
## Copyright (c) Chinmay Deval, 2020
## Email: chinmay.deval91@gmail.com
##
## --------------------------------------------------------------------------------------##
## Notes:
##
##
## --------------------------------------------------------------------------------------##
## ----------------------------------Load packages---------------------------------------##
library(shiny,quietly = TRUE)
library(qs,quietly = TRUE,warn.conflicts = FALSE)
library(tools,quietly = TRUE)
library(sf,quietly = TRUE)
library(tidyverse,quietly = TRUE,warn.conflicts = FALSE)
library(shinythemes,quietly = TRUE)
library(shinycssloaders,quietly = TRUE)
library(shinyWidgets,quietly = TRUE)
library(plotly,quietly = TRUE)
library(stringr,quietly = TRUE)
library(leaflet,quietly = TRUE)
library(tmap,quietly = TRUE)
library(ggthemes,quietly = TRUE)
library(DT,quietly = TRUE)
library(shinyhelper,quietly = TRUE)
library(shinyalert,quietly = TRUE)
library(htmltools,quietly = TRUE)
library(sever,quietly = TRUE)
library(showtext, quietly = TRUE)
library(ragg, quietly = TRUE)
library(thematic, quietly = TRUE)
library(bslib, quietly = TRUE)
source("global.R")
## ----------------------------------Init Options---------------------------------------##
options(shiny.maxRequestSize = 200 * 1024 ^ 2)
thematic_shiny(font = "auto")
ui <- navbarPage(
title = div("Viz-WEPPcloud",
div(
tags$a(
href = "https://forest.moscowfsl.wsu.edu/fswepp/",
tags$img(
src = 'FS.png',
style = "position:fixed;right: 105px;top: 5px;padding-bottom:10px;",
height = 50
)
),
tags$a(
href = "https://www.uidaho.edu/",
tags$img(
src = 'UI.jpg',
style = "position:fixed;right: 150px;top: 5px;padding-bottom:10px;",
height = 50
)
),
tags$a(
href = "https://nifa.usda.gov/",
tags$img(
src = 'nifa.jpg',
style = "position:fixed;right: 60px;top: 5px;padding-bottom:10px;",
height = 50
)
),
tags$a(
href = "https://github.com/devalc/Viz-WEPPcloud",
tags$img(
src = "GitHub-Mark.png",
style = "position:fixed;right: 10px;top: 5px;padding-bottom:10px;",
height = 50
)
)
)),
windowTitle = "Viz-WEPPcloud",
position = "fixed-top",
# fluid = TRUE,
collapsible = TRUE,
id = 'tabs',
header = singleton(tags$head(includeHTML('google-analytics.html'))),
## ----------------------------------Set Theme------------------------------------------##
## set the theme
theme = bslib::bs_theme(bootswatch = "minty",
bg = "#383838",
fg = "#E4E4E4",
primary = "#EA80FC",
secondary = "#00DAC6",
success = "#86d57b",
info = "#28B3ED",
warning = "#FD7424",
danger = "#F7367E",
base_font = font_google("Open Sans"),
heading_font = font_google("Proza Libre"),
code_font = font_google("Fira Code")
),
## ----------------------------------Start defining Tabs------------------------------------------##
## -----------------------------------------Landing Page---------------------------------------------##
tabPanel(
"Home",
icon = icon("home"),
useSever(),
fluidPage(HTML("<br style = 'line-height:10;'><br>"),
HTML("<br>"),
# fluidRow(
div(class = "banner",
tags$style(HTML("
.banner{
position: relative;
background-image: url('banner-bk_g.png');
background-repeat: no-repeat;
background-size: cover;
height: 300px;
border-style: none!important;
}"
)
),
div(class = "bannerright",
# tags$h1("Pi-VAT"),
tags$h2(("An Interactive Watershed Prioritization and Targeting tool for synthesis and decision support using outputs from WEPPcloud.")),
tags$style(HTML("
.bannerright{position: absolute;top: 5%;right: 40%;;left: 21%;
background-color:#3F2D53; color:#fff;transition: margin 10s;}"))
),
div(class = "bannerleft",
tags$img(src= "vizweppcloud_hex_new_cd.svg", height =280)
),
),
HTML("<br/>"),
# column(width = 11,offset = 2,
fluidRow(align = "center",
column(width=4,
align = "centre",
thumbnail_label2(
image = 'background.jpg',
label = 'Watershed Analysis',
content = "Inter-watershed comparison of impacts of management on annual water yield and
water quality at the watershed outlet",
helpinfo = "W_helpinfo"
),
HTML("<br/>"),
actionBttn("Wbutton", "Navigate to Watershed", icon = icon("chart-line"),style = "pill",
color = "royal")
),
column(width=4,
align = "centre",
thumbnail_label2(
image = 'hillslope_img.jpg',
label = 'Hillslope Analysis',
content = "Identifying targeted pollutant hotspots within a watershed and quantifying the impacts of disturbance
and management on the detachment and delivery of pollutants from these hotspots",
helpinfo = "H_helpinfo"
),
HTML("<br/>"),
actionBttn("Hbutton", "Navigate to Hillslope", icon = icon("chart-line"),style = "pill",
color = "royal")
),
column(width=4,
align = "centre",
thumbnail_label2(
image = 'spatial_imp.PNG',
label = 'Spatial Visualization',
content = "Synthesize and visualize hillslope scale output and targeted hotspots across multiple watersheds for multiple treatments",
helpinfo = "S_helpinfo"
),
HTML("<br/>"),
actionBttn("Sbutton", "Navigate to Spatial-Viz", icon = icon("chart-line"),style = "pill",
color = "royal")
# )
),
),
HTML("<br/><br/>"),
div(class = "footer",
tags$style(HTML("
.footer{
position: relative;
background-image: url('footerimg4.jpg');
background-repeat: no-repeat;
background-size: cover;
height: 200px;
border-style: none!important;
margin:0%
}"
)),
div(class = "footerright",
tags$p(
"Viz-WEPPcloud is currently designed to analyze outputs from the online interface for WEPP model (WEPPcloud). It provides users an ability to upload their own runs.",
align = "left"
),
tags$p(
a(href = 'https://wepp1.nkn.uidaho.edu/weppcloud/', 'WEPPcloud', .noWS = "outside"),
' is a cloud based simulation tool based on the process based Watershed Erosion Prediction Project',
tags$a(href="https://www.fs.usda.gov/ccrc/tools/watershed-erosion-prediction-project",
"(WEPP)"), 'model. It estimates
hillslope soil erosion, runoff, and sediment yields from anywhere in the continental U.S. It is especially useful for
post-wildfire assessments, fuel treatment planning, and prescribed fire analysis.',
.noWS = c("after-begin", "before-end"),
align = "left"
),
tags$style(HTML("
.footerright{position: absolute;top: 20%;right: 5%;;left: 40%;color:#fff
}"))
),
div(class = "footerleft",
tags$h3("Powered by",
img(src = "https://www.rstudio.com/wp-content/uploads/2014/04/shiny.png",
height= 60),
"and",
img(src = "https://www.r-project.org/logo/Rlogo.svg",
height= 60),
tags$style(HTML("
.footerleft{position: absolute;top: 20%;right: 60%;;left: 5%;color:#fff
}"))
)
)
)
)
),
## -----------------------------------------Watershed Tab---------------------------------------------##
tabPanel(
"Watershed",
column(
width = 12,
style = 'padding-top:80px;',
# Set up shinyalert
useShinyalert(),
sidebarLayout(
position = "left",
sidebarPanel(
width = 4,
awesomeRadio(
inputId = "DefOrUserUpload_W",
label = "Data Import Options:",
choices = c(
"Default Data (Portland)" = "Default_Data_Portland",
"Default Data (Seattle)" = "Default_Data_Seattle",
"Default Data (Lake Tahoe)" = "Default_Data_LT",
"Default Data (Palouse)" = "Default_Data_Palouse",
"Upload your own data" = "Upload data"
),
selected = "Default_Data_LT",
status = 'success'
),
uiOutput("W_FileInput"),
awesomeRadio(
inputId = "AreaVsScen",
label = "Management/watershed Options: ",
choices = c(
"One Watershed, Selected Scenarios" = "allscen",
"One Scenario, Selected Watersheds" =
"allwat"
),
selected = "allscen",
status = 'success'
),
uiOutput("Wshed_wshed_S"),
uiOutput("Wshed_wshed"),
uiOutput("wshed_var"),
radioGroupButtons(
inputId = "ScenVvar",
label = "Visualization type:",
choices = c("Heatmap" = "Heatmap", "Bar Chart" =
"Bar Chart"),
selected = "Heatmap",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon")),
status = 'success'
),
),
# Main panel for displaying outputs ----
mainPanel(
width = 8,
plotlyOutput("Plot9", height = "700px", width =
"1000px") %>% withSpinner(type = 8 )
)
)
)
),
#
#
# ## -----------------------------------------Hillslope Tab---------------------------------------------##
tabPanel(
"Hillslope",
column(
width = 12,
style = 'padding-top:70px;',
# Set up shinyalert
useShinyalert(),
sidebarLayout(
position = "left",
sidebarPanel(
width = 3,
awesomeRadio(
inputId = "DefOrUserUpload_H",
label = "Data Import Options:",
choices = c(
"Default Data (Portland)" = "Default_Data_Portland",
"Default Data (Seattle)" = "Default_Data_Seattle",
"Default Data (Lake Tahoe)" = "Default_Data_LT",
"Default Data (Palouse)" = "Default_Data_Palouse",
"Upload your own data" =
"Upload data"
),
selected = "Default_Data_LT",
status = 'success'
),
uiOutput("H_FileInput"),
uiOutput("Hill_selectfile"),
uiOutput("Hill_wshed"),
uiOutput("Hill_var"),
uiOutput("Hill_scen_base"),
uiOutput("Hill_scen_comp"),
sliderInput(
"thresh_H",
"Zoom Threshold (%):",
min = 0,
max = 100,
value = 100,
step = NULL,
round = TRUE,
ticks = TRUE,
animate = FALSE
) %>%
helper(
icon = "question-circle",
colour = "#FF0000",
content = "H_plot_thresh",
type = "markdown",
size = "l",
buttonLabel = "Okay",
easyClose = TRUE,
fade = TRUE
),
# uiOutput("Hill_scen"),
radioGroupButtons(
inputId = "summary_DT_by_var_H",
label = "Summarize by:",
choices = c("Land Use" = "Landuse",
"Soil Type" = "Soiltype",
"Both" = "Both"),
selected = "Both",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon")),
status = 'success'
),
),
# Main panel for displaying outputs ----
mainPanel(
width = 9,
tabsetPanel(
tabPanel("Plot",icon =icon("chart-line"), style = 'padding:20px;',
fluidRow(
column(
6,
align = "center",
plotlyOutput("Plot_vs_cumPercArea") %>% withSpinner(type = 8 )
),
column(
6,
align = "center",
plotlyOutput("Plot_vs_cumPercArea_abs") %>% withSpinner(type = 8 )
)
),
# HTML("<br style = “line-height:5;”><br>"),
# uiOutput("Exp3_Exp4") %>% withSpinner(color =
# "#0dc5c1"),
HTML("<br <br>"),
fluidRow(
column(
6,
align = "center",
plotlyOutput("Plot_vs_cumPercLen") %>% withSpinner(type = 8)
),
column(
6,
align = "center",
plotlyOutput("Plot_vs_cumPercLen_abs") %>% withSpinner(type = 8 )
)
)),
tabPanel("Table",icon =icon("table"), style = 'padding:20px;',
# HTML("<br style = “line-height:5;”><br>"),
uiOutput("tab_H")%>% withSpinner(type = 8 )))
)
)
)
),
# ## -----------------------------------------Spatial-Viz Tab---------------------------------------------##
tabPanel(
"Spatial-Viz",
# tags$head(includeHTML((
# "google-analytics.html"
# ))),
style = 'padding-top:70px;',
useShinyalert(),
# Set up shinyalert
sidebarLayout(
sidebarPanel(
width = 3,
awesomeRadio(
inputId = "DefOrUserUpload_S",
label = "Data Import Options:",
choices = c(
"Default Data (Portland)" = "Default_Data_Portland",
"Default Data (Seattle)" = "Default_Data_Seattle",
"Default Data (Lake Tahoe)" = "Default_Data_LT",
"Default Data (Palouse)" = "Default_Data_Palouse",
"Upload your own data" = "Upload data"
),
selected = "Default_Data_LT",
status = 'success'
),
uiOutput("S_FileInput"),
uiOutput("S_FileInput_Chan"),
uiOutput("Spatial_wshed"),
uiOutput("S_var"),
uiOutput("Spatial_scen_base"),
uiOutput("Spatial_scen_comp"),
# uiOutput("Spatial_scen"),
sliderInput(
"thresh_S",
"Zoom Threshold (%):",
min = 0,
max = 100,
value = 100,
step = NULL,
round = TRUE,
ticks = TRUE,
animate = FALSE
) %>%
helper(
icon = "question-circle",
colour = "#FF0000",
content = "S_plot_thresh",
type = "markdown",
size = "l",
buttonLabel = "Okay",
easyClose = TRUE,
fade = TRUE
),
sliderInput(
"thresh_slope_S",
"Slope Threshold:",
min = 0,
max = 1,
value = c(0, 1),
step = NULL,
round = TRUE,
ticks = TRUE,
animate = FALSE
) %>%
helper(
icon = "question-circle",
colour = "#FF0000",
content = "S_slope_thresh",
type = "markdown",
size = "l",
buttonLabel = "Okay",
easyClose = TRUE,
fade = TRUE
),
),
# Main panel for displaying outputs ----
mainPanel(
width = 9,
# style = 'padding:80px;',
tabsetPanel(
tabPanel("Plot",icon =icon("layer-group"), style = 'padding:20px;',
fluidRow(column(
12,
# offset = 1,
leaflet::leafletOutput("Plot12",height = "600px") %>%
withSpinner(type = 8)
))),
tabPanel("Table",icon =icon("table"),style = 'padding:20px;',
# HTML("<br style = “line-height:5;”><br>"),
# fluidRow(column(
# 10,
# offset = 1,
uiOutput("tab_sp") %>%
withSpinner(type = 8)
)),
# HTML("<br style = “line-height:5;”><br>")
)
)
)
)
## ----------------------------------define server logic------------------------------------------##
server <- function(input, output, session) {
## BEtter disconnected screen
sever()
observe({
if (input$DefOrUserUpload_W == 'Upload data') {
shinyalert(
"",
"Please provide the URL pointing to the WEPPCloud watershed file in the Input box",
type = "success"
)
}
})
observe({
if (input$DefOrUserUpload_H == 'Upload data') {
shinyalert(
"",
"Please provide the URL pointing to the WEPPCloud hillslope file in the Input box",
type = "success"
)
}
})
observe({
if (input$DefOrUserUpload_S == 'Upload data') {
shinyalert("", "Please provide the URL pointing to the WEPPCloud spaial file in the Input box", type = "success")
}
})
observeEvent(input$Wbutton, {
updateTabsetPanel(session = session,
inputId = "tabs",
selected = "Watershed")
})
observeEvent(input$Hbutton, {
updateTabsetPanel(session = session,
inputId = "tabs",
selected = "Hillslope")
})
observeEvent(input$Sbutton, {
updateTabsetPanel(session = session,
inputId = "tabs",
selected = "Spatial-Viz")
})
## ----------------------------------Watershed Server logic------------------------------------------##
## ----------------------------------Watershed Server logic------------------------------------------##
######## Server logic for UI generation for Watersheds tab ##########
output$W_FileInput <- renderUI({
if (input$DefOrUserUpload_W == 'Upload data') {
message = 'max. file size is 32MB'
fileInput(
"Wshed_file",
label = "Uplaod 'Watershed' file (*_out_*.csv)",
multiple = F,
placeholder = "No file selected",
accept = ".csv"
)%>%
helper(
icon = "question-circle",
colour = "#FF0000",
content = "W_upload",
type = "markdown",
size = "l",
buttonLabel = "Okay",
easyClose = TRUE,
fade = TRUE
)
} else
if (input$DefOrUserUpload_W == 'Default_Data_Portland' |
input$DefOrUserUpload_W == 'Default_Data_Seattle' |
input$DefOrUserUpload_W == 'Default_Data_LT' |
input$DefOrUserUpload_W == 'Default_Data_Palouse') {
}
})
Wshed_data <- reactive({
req(input$DefOrUserUpload_W)
if (input$DefOrUserUpload_W == 'Default_Data_Portland') {
file3 <- "data/portland202009_out_summary_cd.csv"
read.table(file = file3,
header = TRUE,
sep = ",")
} else
if (input$DefOrUserUpload_W == 'Default_Data_Seattle') {
file3 <- "data/seattle202009_out_summary_cd.csv"
read.table(file = file3,
header = TRUE,
sep = ",")
} else
if (input$DefOrUserUpload_W == 'Default_Data_LT') {
file3 <- "data/lt_202010_out_summary_cd.csv"
read.table(file = file3,
header = TRUE,
sep = ",")
} else
if (input$DefOrUserUpload_W == 'Default_Data_Palouse') {
file3 <- "data/Palouse202103_out_summary.csv"
read.table(file = file3,
header = TRUE,
sep = ",")
} else
if (input$DefOrUserUpload_W == 'Upload data') {
file3 <- input$Wshed_file
if (is.null(file3)) {
return()
}
validate(
need(
grepl("out", input$Wshed_file) == TRUE,
"Wrong file provided. Watershed filename should have '_out_' in filename"
)
)
read.table(
file = file3$datapath,
header = TRUE,
sep = ","
)
}
})
output$Wshed_wshed <- renderUI({
if (input$DefOrUserUpload_W == 'Upload data') {
req(Wshed_data())
if (input$AreaVsScen == 'allscen') {
pickerInput(
"Wshed_wshed",
"Select the watershed of interest",
unique(Wshed_data()$Watershed),
options = list(
`actions-box` = TRUE,
`header` = "Select watershed ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
),
choicesOpt = list(content = stringr::str_trunc(
unique(Wshed_data()$Watershed),
width = 35
))
)
} else
if (input$AreaVsScen == 'allwat') {
pickerInput(
"Wshed_wshed",
"Select the scenario of interest",
unique(Wshed_data()$Scenario),
options = list(
`actions-box` = TRUE,
`header` = "Select scenario ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
}
} else
if (input$DefOrUserUpload_W == 'Default_Data_Portland') {
if (input$AreaVsScen == 'allscen') {
pickerInput(
inputId = "Wshed_wshed",
label = "Select the watershed of interest",
choices = unique(Wshed_data()$Watershed),
selected = unique(Wshed_data()$Watershed)[11],
options = list(
`actions-box` = TRUE,
`header` = "Select watershed ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
} else
if (input$AreaVsScen == 'allwat') {
pickerInput(
"Wshed_wshed",
"Select the scenario of interest",
unique(Wshed_data()$Scenario),
options = list(
`actions-box` = TRUE,
`header` = "Select scenario ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
}
} else
if (input$DefOrUserUpload_W == 'Default_Data_Seattle') {
if (input$AreaVsScen == 'allscen') {
pickerInput(
inputId = "Wshed_wshed",
label = "Select the watershed of interest",
choices = unique(Wshed_data()$Watershed),
selected = unique(Wshed_data()$Watershed)[11],
options = list(
`actions-box` = TRUE,
`header` = "Select watershed ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
} else
if (input$AreaVsScen == 'allwat') {
pickerInput(
"Wshed_wshed",
"Select the scenario of interest",
unique(Wshed_data()$Scenario),
options = list(
`actions-box` = TRUE,
`header` = "Select scenario ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
}
} else
if (input$DefOrUserUpload_W == 'Default_Data_LT') {
if (input$AreaVsScen == 'allscen') {
pickerInput(
inputId = "Wshed_wshed",
label = "Select the watershed of interest",
choices = unique(Wshed_data()$Watershed),
selected = unique(Wshed_data()$Watershed)[11],
options = list(
`actions-box` = TRUE,
`header` = "Select watershed ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
),
choicesOpt = list(content = stringr::str_trunc(
unique(Wshed_data()$Watershed),
width = 35
))
)
} else
if (input$AreaVsScen == 'allwat') {
pickerInput(
"Wshed_wshed",
"Select the scenario of interest",
unique(Wshed_data()$Scenario),
options = list(
`actions-box` = TRUE,
`header` = "Select scenario ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
}
} else
if (input$DefOrUserUpload_W == 'Default_Data_Palouse') {
if (input$AreaVsScen == 'allscen') {
pickerInput(
inputId = "Wshed_wshed",
label = "Select the watershed of interest",
choices = unique(Wshed_data()$Watershed),
selected = unique(Wshed_data()$Watershed)[1],
options = list(
`actions-box` = TRUE,
`header` = "Select watershed ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
} else
if (input$AreaVsScen == 'allwat') {
pickerInput(
"Wshed_wshed",
"Select the scenario of interest",
unique(Wshed_data()$Scenario),
options = list(
`actions-box` = TRUE,
`header` = "Select scenario ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
}
}
})
output$Wshed_wshed_S <- renderUI({
if (input$DefOrUserUpload_W == 'Upload data') {
req(Wshed_data())
if (input$AreaVsScen == 'allscen') {
pickerInput(
"Wshed_wshed_S",
"Select the scenarios of interest",
unique(Wshed_data()$Scenario),
selected = unique(Wshed_data()$Scenario)[1:10],
multiple = TRUE,
options = list(
`actions-box` = TRUE,
`header` = "Select scenarios ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
} else
if (input$AreaVsScen == 'allwat') {
pickerInput(
"Wshed_wshed_S",
"Select the watersheds of interest",
unique(Wshed_data()$Watershed),
selected = unique(Wshed_data()$Watershed)[1:2],
multiple = TRUE,
options = list(
`actions-box` = TRUE,
`header` = "Select watersheds ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
}
} else
if (input$DefOrUserUpload_W == 'Default_Data_Portland') {
if (input$AreaVsScen == 'allscen') {
pickerInput(
"Wshed_wshed_S",
"Select the scenarios of interest",
unique(Wshed_data()$Scenario),
selected = unique(Wshed_data()$Scenario)[1:10],
multiple = TRUE,
options = list(
`actions-box` = TRUE,
`header` = "Select scenarios ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
} else
if (input$AreaVsScen == 'allwat') {
pickerInput(
"Wshed_wshed_S",
"Select the watersheds of interest",
unique(Wshed_data()$Watershed),
selected = unique(Wshed_data()$Watershed)[1:10],
multiple = TRUE,
options = list(
`actions-box` = TRUE,
`header` = "Select watersheds ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
}
} else
if (input$DefOrUserUpload_W == 'Default_Data_Seattle') {
if (input$AreaVsScen == 'allscen') {
pickerInput(
"Wshed_wshed_S",
"Select the scenarios of interest",
unique(Wshed_data()$Scenario),
selected = unique(Wshed_data()$Scenario)[1:10],
multiple = TRUE,
options = list(
`actions-box` = TRUE,
`header` = "Select scenarios ",
`windowPadding` = 1,
`width` = " css-width ",
`size` = 6
)
)
} else
if (input$AreaVsScen == 'allwat') {
pickerInput(
"Wshed_wshed_S",
"Select the watersheds of interest",
unique(Wshed_data()$Watershed),
selected = unique(Wshed_data()$Watershed)[1:10],
multiple = TRUE,