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server.R
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# server.R
# WhaleMap - a Shiny app for visualizing whale survey data
function(input, output, session){
# read in data -------------------------------------------------------
# tracklines
tracks = readRDS('data/processed/effort.rds')
# latest dcs positions
lfile = 'data/processed/dcs_live_latest_position.rds'
if(file.exists(lfile)){
latest = readRDS(lfile)
}
# sightings / detections
observations = readRDS('data/processed/observations.rds')
# dynamic map polygons
load('data/processed/dma.rda')
load('data/processed/sma.rda')
# build date UI -------------------------------------------------------
output$dateChoice <- renderUI({
switch(input$dateType,
'select' = dateInput('date', label = NULL,
value = Sys.Date()),
'range' = dateRangeInput('date', label = NULL,
start = Sys.Date() - tlag, end = Sys.Date()),
'multiyear' = list(
sliderInput('date', label = NULL,
min = as.Date(paste0(cyear,'-01-01')),
max = as.Date(paste0(cyear,'-12-31')),
value = c(Sys.Date()-tlag, Sys.Date()),
step = 1,
timeFormat = '%b-%d',
animate = F),
selectInput('years', label = NULL, choices = seq(cyear,2010,-1),
selected = cyear, multiple = TRUE, selectize = TRUE)
)
)
})
# choose date -------------------------------------------------------
dates <- reactive({
# catch startup error
if(is.null(input$date)){
return(seq(Sys.Date()-tlag, Sys.Date(), 1))
}
# select date from variable inputs
if(input$dateType == 'select'){
input$date
} else if(input$dateType == 'range'){
seq(input$date[1], input$date[length(input$date)], 1)
} else if(input$dateType == 'multiyear'){
# require year (catch startup error)
req(input$years)
# sequence of year days between dates
yd = seq(yday(input$date[1]), yday(input$date[length(input$date)]), 1)
# convert to dates across years
as.Date(
unlist(
lapply(X = input$years, FUN = function(x){
as.Date(yd, origin = paste0(x,'-01-01'))
})),
origin = '1970-01-01')-1
}
})
# choose platform -----------------------------------------------------------
platform <- reactive({
input$platform
})
# name choices -----------------------------------------------------------
# # extract names of active platform(s)
# name_choices <- reactive({
#
# # require date and platform
# req(dates(), platform())
#
# suppressWarnings(
# rbind(tracks[c('date', 'platform', 'name')], observations[c('date', 'platform', 'name')]) %>%
# filter(date %in% dates() & platform %in% platform()) %>%
# pull(name) %>%
# as.character() %>%
# unique()
# )
# })
# build name UI -----------------------------------------------------------
# output$nameChoice <- renderUI({
#
# # construct UI
# selectInput("name", "Choose platform name(s):", multiple = T,
# choices = c('All', name_choices()),
# selected = 'All', selectize = TRUE)
#
# })
# choose name -----------------------------------------------------------
# # name
# name <- reactive({
# if('All' %in% input$name | input$go == 0){
# name_choices()
# } else {
# input$name
# }
# })
# choose data source ------------------------------------------------------
# data source
dsource <- eventReactive(input$go|input$go == 0,{
input$dsource
})
# choose species -----------------------------------------------------------
# species
species <- eventReactive(input$go|input$go == 0,{
input$species
})
# choose colors -----------------------------------------------------------
colorby_obs <- eventReactive(input$go|input$go == 0,{
input$colorby_obs
})
colorby_trk <- eventReactive(input$go|input$go == 0,{
input$colorby_trk
})
pal_obs <- eventReactive(input$go|input$go == 0,{
input$pal_obs
})
pal_trk <- eventReactive(input$go|input$go == 0,{
input$pal_trk
})
# reactive data -----------------------------------------------------------
# subset track data
trk <- eventReactive(input$go|input$go == 0, {
if(input$password == password){
tracks %>%
filter(
date %in% dates() &
source %in% dsource() &
# name %in% name() &
platform %in% platform()
)
} else {
tracks %>%
filter(
date %in% dates() &
source %in% dsource() &
# name %in% name() &
# !(name %in% hidden_platforms)
platform %in% platform()
)
}
})
# subset observation data
obs <- eventReactive(input$go|input$go == 0, {
if(input$password == password){
observations %>%
filter(
date %in% dates() &
source %in% dsource() &
platform %in% platform() &
# name %in% name() &
species %in% species()
) %>%
droplevels()
} else {
observations %>%
filter(
date %in% dates() &
source %in% dsource() &
platform %in% platform() &
species %in% species() &
# name %in% name() &
# !(name %in% hidden_platforms) &
score != 'possible visual'
) %>%
droplevels()
}
})
# only possible
pos <- eventReactive(input$go|input$go == 0, {
obs() %>%
filter(
score %in% c('possible acoustic', 'possible visual')
) %>%
droplevels()
})
# only definite
det <- reactive({
obs() %>%
filter(
score %in% c('definite acoustic', 'definite visual')
) %>%
droplevels()
})
# combine track and observations
allBounds <- reactive({
# combine limits
lat = c(obs()$lat, trk()$lat)
lon = c(obs()$lon, trk()$lon)
# join in list
list(lat, lon)
})
# position for live dcs platform
if(file.exists(lfile)){
LATEST <- eventReactive(input$go|input$go == 0, {
if(input$password == password){
latest %>%
filter(
date %in% dates() &
source %in% dsource() &
# name %in% name() &
platform %in% platform()
)
} else {
latest %>%
filter(
date %in% dates() &
source %in% dsource() &
# name %in% name() &
# !(name %in% hidden_platforms)
platform %in% platform()
)
}
})
}
# release notification ------------------------------------------
# showNotification(
# ui = 'WhaleMap has some new features!',
# action = a(target="_blank", href = "https://whalemap.ocean.dal.ca/features.html", "Check them out here"),
# duration = NULL, closeButton = T, type = 'message')
# warnings --------------------------------------------------------
# password warnings
observeEvent(input$go,{
if(input$password == password){
showNotification(h4('Password was correct! Showing unverified and/or test data...'),
duration = NULL, closeButton = T, type = 'message')
}
})
# general warnings
observeEvent(input$go,{
# track warning
if(nrow(trk())>npts){
showNotification(h4(paste0('Warning! Tracklines have been turned off because
you have attemped to plot too many points (i.e. more than ', as.character(npts), ').
Please select less data to view tracks.')),
duration = 15, closeButton = T, type = 'error')
}
# species warning
if(paste(species(),collapse=',')!='right'){
showNotification(h4('Note: Most real-time reports focus on right whales,
so data on other species may be incomplete.'),
duration = 15, closeButton = T, type = 'error')
}
# year warning
if(min(year(dates()))<2017){
showNotification(h4('Note: Effort data before 2017 are incomplete.'),
duration = 15, closeButton = T, type = 'error')
}
})
# colorpals -----------------------------------------------------------------
# define color palette for any column variable
colorpal_obs <- reactive({
# extract factor levels
n = unique(obs()[,which(colnames(obs())==colorby_obs())])
if(colorby_obs() %in% c('yday', 'lat', 'lon')){
# use continuous palette
colorNumeric(get_palette(pal = pal_obs(), n = length(n)), domain = n)
} else if (colorby_obs() == 'number'){
if(is.infinite(min(obs()$number, na.rm = T))){
# define colorbar limits if 'number' is selected without sightings data
colorNumeric(get_palette(pal = pal_obs(), n = length(n)),
c(NA,0), na.color = 'darkgrey')
} else {
# use continuous palette
colorNumeric(get_palette(pal = pal_obs(), n = length(n)),
obs()$number, na.color = 'darkgrey')
}
} else if (colorby_obs() == 'score' & pal_obs() == 'Default'){
# hard wire colors for score factor levels
colorFactor(levels = c('definite acoustic', 'possible acoustic', 'possible visual', 'definite visual'),
palette = c('red', 'yellow', 'grey', 'darkslategrey'))
} else {
# color by factor level
colorFactor(get_palette(pal_obs(), length(n)), n)
}
})
# define color palette for any column variable
colorpal_trk <- reactive({
if(colorby_trk() == 'platform' & pal_trk() == 'Default'){
# hardwire colors for score factor levels
colorFactor(
levels = names(platform_cols),
palette = as.character(platform_cols)
)
} else {
# extract factor levels
n = unique(trk()[,which(colnames(trk())==colorby_trk())])
# color by factor level
colorFactor(get_palette(pal = pal_trk(), n = length(n)), levels = n)
}
})
# basemap -----------------------------------------------------------------
output$map <- renderLeaflet({
leaflet(tracks) %>%
fitBounds(~max(lon, na.rm = T),
~min(lat, na.rm = T),
~min(lon, na.rm = T),
~max(lat, na.rm = T)) %>%
# add extra map features
addScaleBar(position = 'topright')%>%
addFullscreenControl(pseudoFullscreen = TRUE) %>%
addMeasure(
primaryLengthUnit = "kilometers",
secondaryLengthUnit = 'miles',
primaryAreaUnit = "hectares",
secondaryAreaUnit="acres",
activeColor = "#006622",
completedColor = "#004d1a",
position = 'bottomleft')
# addControlGPS(options = gpsOptions(position = "topleft", activate = FALSE,
# autoCenter = TRUE, maxZoom = 8,
# setView = TRUE))
})
# tile observer ------------------------------------------------------
observeEvent(input$basemap, {
# add tile
leafletProxy("map") %>%
clearTiles() %>%
addProviderTiles(providers[[input$basemap]], layerId = 'basemap')
})
# graticules ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('graticules')
if(input$graticules){
# add graticules
proxy %>%
addSimpleGraticule(zoomIntervals = graticule_ints,
group = 'graticules',
showOriginLabel = FALSE)
# switch to show/hide
ifelse(input$graticules, showGroup(proxy, 'graticules'),
hideGroup(proxy, 'graticules'))
}
})
# noaa charts ------------------------------------------------------
# observe(priority = 4, {
#
# # define proxy
# proxy <- leafletProxy("map")
# proxy %>% clearGroup('noaa')
#
# if(input$noaa){
#
# # add noaa charts
# proxy %>%
# addWMSTiles(baseUrl = "https://gis.charttools.noaa.gov/arcgis/rest/services/MCS/ENCOnline/MapServer/exts/MaritimeChartService/WMSServer")
# # addTiles(urlTemplate = '//tileservice.charts.noaa.gov/tiles/50000_1/{z}/{x}/{y}.png', group = 'noaa')
#
# # switch to show/hide
# ifelse(input$noaa, showGroup(proxy, 'noaa'),
# hideGroup(proxy, 'noaa'))
# }
#
# })
# critical habitat zone ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('critical_habitat_zone')
if(input$critical_habitat_zone){
# add mpas
proxy %>%
addPolygons(data=critical_habitat_zone,
group = 'critical_habitat_zone',
fill = T,
fillOpacity = 0.25,
stroke = T,
dashArray = c(5,5),
options = pathOptions(clickable = F),
weight = 1,
color = 'darkgreen',
fillColor = 'darkgreen')
# switch to show/hide
ifelse(input$critical_habitat_zone, showGroup(proxy, 'critical_habitat_zone'),
hideGroup(proxy, 'critical_habitat_zone'))
}
})
# dfo zone observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('dfo_zone')
if(input$dfo_zone){
# add polygons
proxy %>%
addPolygons(data=dfo_zone, group = 'dfo_zone',
fill = T,
fillOpacity = 0.25,
stroke = T,
dashArray = c(5,5),
options = pathOptions(clickable = T),
popup = ~paste0(ID),
weight = 1,
color = 'darkblue',
fillColor = 'darkblue')
# switch to show/hide
ifelse(input$dfo_zone, showGroup(proxy, 'dfo_zone'),
hideGroup(proxy, 'dfo_zone'))
}
})
# dfo lines observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('dfo_lines')
if(input$dfo_lines){
# add polygons
proxy %>%
addPolylines(data=dfo_10f, group = 'dfo_lines',
options = pathOptions(clickable = F),
weight = 1,
dashArray = c(1,1),
color = 'darkblue') %>%
addPolylines(data=dfo_20f, group = 'dfo_lines',
options = pathOptions(clickable = F),
dashArray = c(5,5),
weight = 1,
color = 'darkblue')
# switch to show/hide
ifelse(input$dfo_lines, showGroup(proxy, 'dfo_lines'),
hideGroup(proxy, 'dfo_lines'))
}
})
# full grid observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('full_grid')
if(input$full_grid){
# add polygons
proxy %>%
addPolygons(data = full_grid,
color = 'grey',
group = 'full_grid',
weight = 2,
smoothFactor = 3,
popup = ~paste0(Grid_Index))
# switch to show/hide
ifelse(input$full_grid, showGroup(proxy, 'full_grid'),
hideGroup(proxy, 'full_grid'))
}
})
# tc zone observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('tc_zone')
if(input$tc_zone){
# add polygons
proxy %>%
addPolygons(data=tc_zone, group = 'tc_zone',
fill = T,
fillOpacity = 0.25,
stroke = T,
dashArray = c(5,5),
options = pathOptions(clickable = T),
popup = ~paste0(ID),
weight = 1,
color = 'darkgreen',
fillColor = 'darkgreen')
# switch to show/hide
ifelse(input$tc_zone, showGroup(proxy, 'tc_zone'),
hideGroup(proxy, 'tc_zone'))
}
})
# tc ra observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('tc_ra')
if(input$tc_ra){
# add polygons
proxy %>%
addPolygons(data=tc_ra, group = 'tc_ra',
fill = T,
fillOpacity = 0.25,
stroke = T,
dashArray = c(5,5),
options = pathOptions(clickable = F),
weight = 1,
color = 'orange',
fillColor = 'orange')
# switch to show/hide
ifelse(input$tc_ra, showGroup(proxy, 'tc_ra'),
hideGroup(proxy, 'tc_ra'))
}
})
# tss observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('tss')
if(input$tss){
# plot shipping lanes
proxy %>%
addPolylines(tss_lines$lon, tss_lines$lat,
weight = .5,
color = 'grey',
options = pathOptions(clickable = F),
group = 'tss') %>%
addPolygons(tss_polygons$lon, tss_polygons$lat,
weight = .5,
color = 'grey',
fillColor = 'grey',
options = pathOptions(clickable = F),
group = 'tss') %>%
addPolygons(data = tss_usa,
weight = .5,
color = 'grey',
fillColor = 'grey',
options = pathOptions(clickable = F),
group = 'tss')
# switch to show/hide
ifelse(input$tss, showGroup(proxy, 'tss'), hideGroup(proxy, 'tss'))
}
})
# US lobster observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('us_lobster')
if(input$us_lobster){
# add polygons
proxy %>%
addPolygons(data=us_lobster, group = 'us_lobster',
fill = T,
fillOpacity = 0.25,
stroke = T,
popup = ~paste0(COMMNAME),
weight = 1,
color = 'blue',
fillColor = 'blue')
# switch to show/hide
ifelse(input$us_lobster, showGroup(proxy, 'us_lobster'),
hideGroup(proxy, 'us_lobster'))
}
})
# US BOEM observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('boem')
if(input$boem){
# add polygons
proxy %>%
addPolygons(data=boem, group = 'boem',
fill = T,
fillOpacity = 0.25,
stroke = T,
popup = ~paste0(ID),
weight = 1,
color = 'green',
fillColor = 'green')
# switch to show/hide
ifelse(input$boem, showGroup(proxy, 'boem'),
hideGroup(proxy, 'boem'))
}
})
# dma observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('dma')
# add polygons
proxy %>%
addPolygons(data=dma, group = 'dma',
fill = T,
fillOpacity = 0.3,
stroke = T,
dashArray = c(5,5),
options = pathOptions(clickable = T),
popup = ~paste(sep = "<br/>" ,
"US Slow Zone",
paste0(NAME),
# paste0("Type: ", triggertype),
paste0("Expires: ", EXPDATE)),
weight = 1,
color = '#ff9900',
fillColor = '#ff9900')
# switch to show/hide
ifelse(input$dma, showGroup(proxy, 'dma'),
hideGroup(proxy, 'dma'))
})
# sma observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('sma')
if(input$sma){
# add polygons
proxy %>%
addPolygons(data=sma, group = 'sma',
fill = T,
fillOpacity = 0.3,
stroke = T,
options = pathOptions(clickable = T),
popup = ~paste(sep = "<br/>" ,
"US Seasonal Management Area",
paste0(NAME)),
weight = 1,
color = 'red',
fillColor = 'red')
# switch to show/hide
ifelse(input$sma, showGroup(proxy, 'sma'),
hideGroup(proxy, 'sma'))
}
})
# alwtrp observer ------------------------------------------------------
observe(priority = 4, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('alwtrp')
if(input$alwtrp){
# add polygons
proxy %>%
addPolygons(data=alwtrp, group = 'alwtrp',
fill = T,
fillOpacity = 0.3,
stroke = T,
options = pathOptions(clickable = T),
popup = ~paste(sep = "<br/>" ,
"US fishery seasonal restricted area",
paste0(ID),
paste0('Active: ', ACTIVE)),
weight = 1,
color = 'brown2',
fillColor = 'brown2')
# switch to show/hide
ifelse(input$alwtrp, showGroup(proxy, 'alwtrp'),
hideGroup(proxy, 'alwtrp'))
}
})
# track observer ------------------------------------------------------
# observe(priority = 3, {
observeEvent(input$tracks|input$go|input$go == 0, priority = 3, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('tracks')
# tracks
if(input$tracks & nrow(trk())<npts){
# set up polyline plotting
tracks.df <- split(trk(), trk()$id)
# get color palette
pal = colorpal_trk()
ind = which(colnames(trk())==colorby_trk())
# add lines
names(tracks.df) %>%
purrr::walk( function(df) {
proxy <<- proxy %>%
addPolylines(data=tracks.df[[df]],
group = 'tracks',
lng=~lon,
lat=~lat,
weight = 2,
smoothFactor = 1,
options = markerOptions(removeOutsideVisibleBounds=TRUE, opacity = 0.5),
color = pal(tracks.df[[df]][1,ind]),
popup = paste0('Track ID: ', unique(tracks.df[[df]]$id)))
})
# set up buoy plotting
buoy.df <- trk() %>%
filter(platform == 'buoy') %>%
arrange(time) %>%
group_by(id) %>%
dplyr::slice(1)
buoy.df <- split(buoy.df, buoy.df$id)
# add circles
names(buoy.df) %>%
purrr::walk( function(df) {
proxy <<- proxy %>%
addCircleMarkers(data=buoy.df[[df]],
radius = 6,
opacity = 1,
stroke = T,
fill = T,
fillOpacity = 0,
weight = 2.5,
group = 'tracks',
lng=~lon,
lat=~lat,
color = pal(tracks.df[[df]][1,ind]),
popup = paste0('Track ID: ', unique(tracks.df[[df]]$id)))
})
}
})
# latest observer ------------------------------------------------------
if(file.exists(lfile)){
observe(priority = 3, {
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('latest')
# tracks
if(input$latest){
# add icons for latest position of live dcs platforms
proxy %>%
addMapPane("lts", zIndex = 350) %>%
addMarkers(data = LATEST(), ~lon, ~lat,
icon = ~dcsIcons[platform],
options=pathOptions(pane = "lts"),
popup = ~paste(sep = "<br/>",
strong('Latest position'),
paste0('Platform: ', as.character(platform)),
paste0('Name: ', as.character(name)),
paste0('Time: ', as.character(time), ' UTC'),
paste0('Position: ',
as.character(lat), ', ', as.character(lon))),
label = ~paste0('Latest position of ', as.character(name), ': ',
as.character(time), ' UTC'), group = 'latest')
}
})
}
# possible observer ------------------------------------------------------
observe(priority = 2,{
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('possible')
if(input$possible){
# set up color palette plotting
pal <- colorpal_obs()
# possible detections
addCircleMarkers(map = proxy, data = pos(), ~lon, ~lat, group = 'possible',
radius = 4, fillOpacity = 0.9, stroke = T, col = 'black', weight = 0.5,
fillColor = pal(pos()[,which(colnames(pos())==colorby_obs())]),
popup = ~paste(sep = "<br/>" ,
paste0("Species: ", species),
paste0("Score: ", score),
paste0("Number: ", number),
paste0("Calves: ", calves),
paste0("Platform: ", platform),
paste0("Name: ", name),
paste0("Date: ", as.character(date)),
paste0("Time: ", as.character(format(time, '%H:%M:%S UTC'))),
paste0("Position: ", as.character(lat), ', ', as.character(lon)),
paste0("Source: ", source)),
options = markerOptions(removeOutsideVisibleBounds=T))
}
})
# definite observer ------------------------------------------------------
observe(priority = 1,{
# define proxy
proxy <- leafletProxy("map")
proxy %>% clearGroup('detected')
if(input$detected){
# set up color palette plotting
pal <- colorpal_obs()
# definite detections
addCircleMarkers(map = proxy, data = det(), ~lon, ~lat, group = 'detected',
radius = 4, fillOpacity = 0.9, stroke = T, col = 'black', weight = 0.5,
fillColor = pal(det()[,which(colnames(det())==colorby_obs())]),
popup = ~paste(sep = "<br/>" ,
paste0("Species: ", species),
paste0("Score: ", score),
paste0("Number: ", number),
paste0("Calves: ", calves),
paste0("Platform: ", platform),
paste0("Name: ", name),
paste0("Date: ", as.character(date)),
paste0("Time: ", as.character(format(time, '%H:%M:%S UTC'))),
paste0("Position: ", as.character(lat), ', ', as.character(lon)),
paste0("Source: ", source)),
options = markerOptions(removeOutsideVisibleBounds=T))
}
})
# legend observer ------------------------------------------------------
observe({
# define proxy
proxy <- leafletProxy("map")