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SPoT_app.R
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SPoT_app.R
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## To deploy to shinyapps.io, include:
## - this script
## - all of the files in the 'data_processed' folder
## (no other files need to be published - e.g., don't need to publish the
## 'data_raw' folder)
# load packages -----------------------------------------------------------
library(shiny)
library(shinyjs)
library(shinycssloaders)
library(shinyWidgets)
library(tidyverse)
library(sf)
library(leaflegend)
library(leaflet)
library(glue)
library(janitor)
library(here)
library(FedData)
## conflicts ----
library(conflicted)
conflicts_prefer(dplyr::filter)
# setup -------------------------------------------------------------------
## coordinate systems for transformations
projected_crs <- 3310 # see: https://epsg.io/3310
# other options: 26910 see: https://epsg.io/26910
# resources:
# https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=109326&inline
#
geographic_crs <- 4269 # see: https://epsg.io/4269
# see: https://epsg.io/4326
# load data ----------------------------------------------------------------
## SPoT catchments ----
spot_catchments <- st_read(here('data_processed',
'spot_catchments_2019-03-04.gpkg'))
## SPoT sites ----
spot_sites <- st_read(here('data_processed',
'spot_sites.gpkg')) %>%
mutate(location_color = as.factor(location_color))
## CalEnviroScreen 4 ----
ces_4 <- st_read(here('data_processed',
'calenviroscreen_4-0.gpkg')) %>%
mutate(c_iscore = case_when(c_iscore == -999 ~ NA,
TRUE ~ c_iscore),
c_iscore_p = case_when(c_iscore_p == -999 ~ NA,
TRUE ~ c_iscore_p))
## tribal boundaries ----
tribal_bounds_bia <- st_read(here('data_processed',
'ca_tribal_boundaries_bia.gpkg'))
## CA boundary ----
ca_boundary <- st_read(here('data_processed',
'ca_boundary.gpkg'))
## NLCD ----
nlcd_legend <- nlcd_colors() %>%
filter(!str_detect(string = Description, pattern = 'Alaska only')) %>%
select(Class, Color)
# web services ------------------------------------------------------------
## NLCD (see: https://www.mrlc.gov/data-services-page AND more generally: https://www.mrlc.gov/data/nlcd-2019-land-cover-conus)
wms_nlcd <- 'https://www.mrlc.gov/geoserver/mrlc_display/NLCD_2019_Land_Cover_L48/wms?service=WMS&'
# define UI ---------------------------------------------------------------
ui <- fillPage(
leafletOutput('spot_map_render', height = "100%") %>%
# withSpinner(color="#0dc5c1") %>% # not working
addSpinner(color = '#0dc5c1',
spin = 'double-bounce' # 'fading-circle' 'rotating-plane'
) %>%
{.}
)
# Define server logic -----------------------------------------------------
server <- function(input, output) {
## create leaflet map ----
output$spot_map_render <- renderLeaflet({
### create empty map ----
spot_map <- leaflet()
### set initial zoom ----
spot_map <- spot_map %>%
setView(lng = -119.5, # CA centroid: -119.5266
lat = 37.5, # CA centroid: 37.15246
zoom = 6)
### add basemap options ----
basemap_options <- c( # NOTE: use 'providers$' to see more options
#'Stamen.TonerLite',
'CartoDB.Positron',
'Esri.WorldTopoMap',
# 'Esri.WorldGrayCanvas',
'Esri.WorldImagery'#,
# 'Esri.WorldStreetMap'
)
for (provider in basemap_options) {
spot_map <- spot_map %>%
addProviderTiles(provider,
group = provider,
options = providerTileOptions(noWrap = TRUE))
}
### add panes ----
#### (sets the order in which layers are drawn/stacked -- higher
#### numbers appear on top)
spot_map <- spot_map %>%
addMapPane('nlcd_pane', zIndex = 480) %>%
addMapPane('nlcd_ca_pane', zIndex = 490) %>%
addMapPane('ces_4_pane', zIndex = 500) %>%
addMapPane('tribal_boundaries_pane', zIndex = 510) %>%
addMapPane('spot_catchments_pane', zIndex = 520) %>%
addMapPane('spot_sites_pane', zIndex = 530) %>%
{.}
### add legend for Tribal Boundaries ----
spot_map <- spot_map %>%
addLegend(position = 'bottomright',
colors = 'blueviolet',
labels = 'Tribal Area',
opacity = 1,
layerId = 'tribal_areas_legend',
group = 'Tribal Areas')
### add legend for SPoT catchments ----
spot_map <- spot_map %>%
addLegendSymbol(values = 'SPoT Catchment',
color = 'dodgerblue',
shape = 'line',
strokeWidth = 2,
group = 'SPoT Catchments',
position = 'bottomright')
### add SPoT sites ----
#### add legend for SPoT sites shapes / borders
spot_map <- spot_map %>%
addLegendSymbol(values = 'CEC Sampling Sites',
shape = 'circle',
fillColor = 'white',
width = 20,
color = '#03F',
strokeWidth = 8,
opacity = 0.7,
group = 'SPoT Sites',
position = 'bottomright')
#### Create color palette for SPoT toxicity scores
site_colors <- c('red', 'orange', 'yellow', 'green', 'black')
spot_sites_pal <- colorFactor(
palette = site_colors,
domain = spot_sites$location_color,
levels = c(1, 2, 3, 4, 5)
)
#### add legend for SPoT colors
spot_map <- spot_map %>%
addLegend(position = 'bottomright',
colors = site_colors,
labels = c('0 - 80', '80 - 90', '90 - 95', '95 - 100+', 'DPR Locations'),
opacity = 1,
layerId = 'sites_legend',
group = 'SPoT Sites',
title = paste0('SPoT Sites Avg Tox Response'))
#### add SPoT sites
spot_map <- spot_map %>%
addCircleMarkers(data = spot_sites %>%
st_transform(crs = geographic_crs),
options = pathOptions(pane = 'spot_sites_pane'),
radius = 5,
stroke = TRUE,
weight = ~ifelse(possible_sample_loc == 'yes',
4,
1),
color = ~ifelse(possible_sample_loc == 'yes',
'#03F',
'black'),
opacity = ~ifelse(possible_sample_loc == 'yes',
0.8, # 1,
0.6),
fill = TRUE,
fillOpacity = 1,
fillColor = ~ spot_sites_pal(location_color),
# highlightOptions = highlightOptions(color = "red", weight = 2, bringToFront = TRUE),
popup = ~paste0('<b>', '<u>', 'SPoT Site', '</u>', '</b>','<br/>',
'<b>', 'Station Name: ', '</b>', station_name, '<br/>',
'<b>', 'Station Code: ', '</b>', station_code, '<br/>',
'<b>', 'Average Toxicity (2008-2022): ', '</b>', round(average_toxicity_2008_2022, 2), '<br/>',
'<b>', 'Possible Sample Location: ', '</b>', possible_sample_loc, '<br/>'
),
group = 'SPoT Sites',
label = ~glue('SPoT Site (Station Name: {station_name})'))
### add SPoT catchments ----
spot_map <- spot_map %>%
addPolylines(data = spot_catchments %>%
st_transform(crs = geographic_crs), # have to convert to geographic coordinate system for leaflet)
options = pathOptions(pane = 'spot_catchments_pane'),
color = 'dodgerblue',
weight = 1.0,
smoothFactor = 1.0,
opacity = 0.7,
fill = FALSE,
fillOpacity = 0.4,
fillColor = 'lightgrey',
highlightOptions = highlightOptions(color = "darkblue",
weight = 2,
bringToFront = TRUE),
popup = ~paste0('<b>', '<u>', 'SPoT Catchment', '</u>', '</b>','<br/>',
'<b>', 'Station Name: ', '</b>', station_nam, '<br/>',
'<b>', 'Station Code: ', '</b>', station_cod, '<br/>'#,
),
group = 'SPoT Catchments',
label = ~glue('SPoT Catchment ({station_nam})')
)
### add CalEnviroScreen (CES) ----
#### Create color palette for CES scores
ces_pal <- colorNumeric(
palette = 'RdYlGn',
domain = ces_4$c_iscore_p,
reverse = TRUE)
#### add CES polygons
spot_map <- spot_map %>%
addPolygons(data = ces_4 %>%
st_transform(crs = geographic_crs),
options = pathOptions(pane = "ces_4_pane"),
color = 'darkgrey',
weight = 0.5,
smoothFactor = 1.0,
opacity = 0.8,
fillOpacity = 0.8,
fillColor = ~ces_pal(c_iscore_p),
highlightOptions = highlightOptions(color = "white", weight = 2),
popup = ~paste0('<b>', '<u>','CalEnviroScreen 4.0 (CES)', '</u>','</b>','<br/>',
'<b>', 'Census Tract: ', '</b>', tract, '<br/>',
'<b>', 'CES Score: ', '</b>', round(c_iscore, 2), '<br/>',
'<b>', 'CES Percentile: ', '</b>', round(c_iscore_p, 2), '<br/>'),
group = 'CalEnviroScreen 4.0'#,
# label = ~glue('CES 4.0 (Percentile: {round(c_iscore_p, 2)})')
)
#### add CES legend
spot_map <- spot_map %>%
addLegend(position = 'bottomleft',
pal = ces_pal,
values = ces_4$c_iscore_p,
opacity = 1,
layerId = 'ces_legend',
bins = 4,
group = 'CalEnviroScreen 4.0',
title = 'CalEnviroScreen 4.0 Percentile'
)
### add tribal boundaries ----
spot_map <- spot_map %>%
addPolygons(data = tribal_bounds_bia %>%
st_transform(crs = geographic_crs),
options = pathOptions(pane = "tribal_boundaries_pane"),
color = 'darkgrey',
weight = 0.5,
smoothFactor = 1.0,
opacity = 0.8,
fillOpacity = 0.8,
fillColor = 'blueviolet',
highlightOptions = highlightOptions(color = "white", weight = 2),
popup = ~paste0('<b>', '<u>','Tribal Area', '</u>','</b>','<br/>',
'<b>', 'Name: ', '</b>', larname, '<br/>'#,
# '<b>', 'Agency: ', '</b>', agency, '<br/>',
),
group = 'Tribal Areas',
label = ~glue('Tribal Area ({larname})')
)
### add NLCD (land cover) ----
#### (NOTE: the legend is added below via leafletProxy, so that the legend
#### doesn't show up when the map is first rendered)
spot_map <- spot_map %>%
addWMSTiles(
wms_nlcd,
layers = 'NLCD_2019_Land_Cover_L48',
options = c(WMSTileOptions(format = 'image/png', transparent = TRUE),
pathOptions(pane = 'nlcd_pane')),
attribution = 'National Land Cover Database 2019',
group = 'Land Cover (2019 NLCD)') %>%
## add the CA boundary on top of the NLCD layer
addPolylines(data = ca_boundary %>%
st_transform(crs = geographic_crs), # have to convert to geographic coordinate system for leaflet)
options = pathOptions(pane = 'nlcd_ca_pane'),
color = 'black',
weight = 1.0,
smoothFactor = 1.0,
opacity = 0.7,
group = 'Land Cover (2019 NLCD)',
label = 'CA Boundary') %>%
hideGroup('Land Cover (2019 NLCD)')
### add layer controls ----
spot_map <- spot_map %>%
addLayersControl(baseGroups = basemap_options,
overlayGroups = c(
'CalEnviroScreen 4.0',
'SPoT Sites',
'SPoT Catchments',
'Tribal Areas',
'Land Cover (2019 NLCD)'
),
options = layersControlOptions(collapsed = TRUE,
autoZIndex = TRUE))
})
## add NLCD legend ----
### (have to do this with leafletProxy so that the legend doesn't show up
### when the map is first rendered)
observe({
# observeEvent(input$spot_map_render_groups,{
if ('Land Cover (2019 NLCD)' %in% input$spot_map_render_groups){
leafletProxy('spot_map_render') %>%
addLegend(position = 'bottomleft',
colors = nlcd_legend$Color,
labels = nlcd_legend$Class,
opacity = 1,
layerId = 'nlcd_legend',
group = 'Land Cover (2019 NLCD)',
title = 'Land Cover Classes (NLCD)')
}
})
}
# run application --------------------------------------------------------
shinyApp(ui = ui, server = server)