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server.R
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library(leaflet)
library(shiny)
library(shinyjs)
library(sp)
library(raster)
library(rgdal)
library(rgeos)
library(Cairo)
library(RColorBrewer)
### LOAD ADDING FUNCTIONS ------------------------------------------------------
fls <- list.files(
path = "R",
pattern = "\\.R$",
full.names = TRUE
)
tmp <- sapply(fls, source, .GlobalEnv)
rm(list = c("fls", "tmp"))
### LOAD DATASETS --------------------------------------------------------------
data_species <- readRDS("data/infos/species_list.rds")
data_climate <- readRDS("data/infos/variables_list.rds")
data_ecosystem <- readRDS("data/infos/ecosystem_list.rds")
data_network <- readRDS("data/infos/network_list.rds")
data_vulnerability <- data_network[which(data_network[ , "code"] == "Net01"), ]
data_network <- data_network[which(data_network[ , "code"] != "Net01"), ]
grd <- readRDS("data/background/grid.rds")
grd_tundra <- readRDS("data/background/grid_tundra.rds")
### AVAILABLE RAMP COLORS ------------------------------------------------------
rampcolors <- data.frame(
palette = rownames(brewer.pal.info),
maxcolors = brewer.pal.info[ , "maxcolors"],
stringsAsFactors = FALSE
)
### CAIRO FONTS ----------------------------------------------------------------
cairoFont <- "Times New Roman"
CairoFonts(
regular = paste0(cairoFont, ":style=Regular"),
bold = paste0(cairoFont, ":style=Bold"),
italic = paste0(cairoFont, ":style=Italic"),
bolditalic = paste0(cairoFont, ":style=Bold Italic,BoldItalic")
)
server <- function(input, output, session) {
### HIDE LIST OF COLOR PALETTES ----------------------------------------------
observe({
for (i in c("climate", "species", "ecosystem", "network", "vulnerability")) {
hide(id = paste0("color_", i))
}
})
### CATCH SELECTED TAB ------------------------------------------------------
suffix <- reactive({
gsub(
"tab_",
"",
reactive({
input$nav
})()
)
})
### SET APPROPRIATED DATASET ------------------------------------------------
data <- reactive({
if (suffix() == "climate") {
data_climate
} else {
if (suffix() == "species") {
data_species
} else {
if (suffix() == "ecosystem") {
data_ecosystem
} else {
if (suffix() == "network") {
data_network
} else {
if (suffix() == "vulnerability") {
data_vulnerability
} else {
NULL
}
}
}
}
}
})
### DEFINE LEAFLET STUDY AREA -----------------------------------------------
area <- reactive({
if (suffix() %in% c("species", "climate")) {
grd
} else {
grd_tundra
}
})
### DEFINE LEAFLET ZOOM LEVEL -----------------------------------------------
coords <- reactive({
if (suffix() %in% c("species", "climate")) {
c(-45.50, 51.00, -75.50, 62.50)
} else {
c(-66.00, 55.65, -74.00, 63.25)
}
})
### FIRST DISPLAY OF LEAFLET MAPS (ON APP OPENNING) --------------------------
for (map in c("map_species", "map_climate", "map_ecosystem", "map_network", "map_vulnerability")) {
output[[map]] <- renderLeaflet({
leaflet(
data = area()
) %>%
addProviderTiles(
provider = providers$Esri.WorldTopoMap
) %>%
addPolygons(
color = "#8e501d",
weight = 2,
opacity = 1.0,
fillOpacity = 0,
fillColor = "transparent"
) %>%
fitBounds(
lng1 = ~coords()[1],
lat1 = ~coords()[2],
lng2 = ~coords()[3],
lat2 = ~coords()[4]
) %>%
addEasyButton(
easyButton(
icon = "fa-globe",
title = "Zoom to study area",
onClick = JS(
paste0(
"function(btn, ", map, "){ ",
map, ".fitBounds(",
"[[",
coords()[2], ", ", coords()[3],
"], [",
coords()[4], ", ", coords()[1],
"]]); }"
)
)
)
) %>%
addMiniMap(
position = "bottomleft",
tiles = providers$Esri.WorldTopoMap,
toggleDisplay = TRUE
)
})
}
### CATCH SELECTED LANGUAGE --------------------------------------------------
langue <- reactive({
if (suffix() %in% c("climate", "species", "network")) {
input[[paste0("language_", suffix())]]
} else {
NULL
}
})
### GET VARIABLE NAMES COLUMNS -----------------------------------------------
columns <- reactive({
if (suffix() == "species") {
c("common_en", "common_fr", "latin", "inuktitut")
} else {
if (suffix() %in% c("climate", "network")) {
c("english", "french")
} else {
"english"
}
}
})
### CATCH SELECTED SPECIES GROUP ---------------------------------------------
spclass <- reactive({
if (suffix() %in% c("species", "ecosystem")) {
input[[paste0("class_", suffix())]]
} else {
NULL
}
})
### GET VARIABLES LIST FOR THE SELECTED LANGUAGE -----------------------------
var_list <- reactive({
if (suffix() %in% c("climate", "species", "network")) {
if (suffix() %in% c("climate", "network")) {
rows <- 1:nrow(data())
empty <- c("Select a variable" = "")
} else {
rows <- which(data()[ , "class"] == spclass())
empty <- c("Select a species" = "")
}
c(empty, sort(as.character(data()[rows, langue()])))
} else {
NULL
}
})
### GET SELECTED VARIABLE (translate if required) ----------------------------
var_selected <- reactive({
if (suffix() %in% c("climate", "species", "network")) {
# If no species/variable selected (RESET MAP)
if (input[[paste0("select_", suffix())]] == "") {
NULL
} else {
# If different species/variable in the same language (UPDATE MAP)
if (length(which(var_list() == input[[paste0("select_", suffix())]])) == 1) {
input[[paste0("select_", suffix())]]
} else {
# If same language but different class (RESET MAP) [only for species tab]
if (length(which(data()[ , langue()] == input[[paste0("select_", suffix())]])) == 1) {
NULL
# If same species/variable in a different language
} else {
pos <- NULL
for (i in columns()) {
if (length(which(data()[ , i] == input[[paste0("select_", suffix())]])) > 0) {
pos <- which(data()[ , i] == input[[paste0("select_", suffix())]])
}
}
pos <- which(var_list() == data()[pos, langue()])
# If match found (SAME MAP)
if (length(pos) == 1) {
var_list()[pos]
# If no correspondance found (RESET MAP) [Inuktituk]
} else {
NULL
}
}
}
}
} else {
if (suffix() == "ecosystem") {
"radio"
} else {
if (suffix() == "vulnerability") {
"Vulnerability index"
} else {
NULL
}
}
}
})
### GET VARIABLE UNITS (for exported map legend) -----------------------------
var_units <- reactive({
if (!is.null(var_selected())) {
if (suffix() == "climate") {
pos <- NULL
for (i in columns()) {
if (length(which(data()[ , i] == var_selected())) == 1) {
pos <- which(data()[ , i] == var_selected())
}
}
unit <- as.character(data()[pos, "units"])
if (unit == "-") {
NULL
} else {
as.character(data()[pos, "units"])
}
} else {
NULL
}
} else {
NULL
}
})
### GET SELECTED TIME PERIOD -------------------------------------------------
period <- reactive({
if (suffix() %in% c("climate", "species", "ecosystem", "network", "vulnerability")) {
input[[paste0("horizon_", suffix())]]
} else {
NULL
}
})
### GET SELECTED RCP (adapt depending on time period) ------------------------
rcp <- reactive({
if (suffix() %in% c("climate", "species", "ecosystem", "network", "vulnerability")) {
if (period() == "1981-2010") {
NULL
} else {
if (is.null(input[[paste0("scenario_", suffix())]])) {
paste0("rcp45_", suffix())
} else {
input[[paste0("scenario_", suffix())]]
}
}
} else {
NULL
}
})
### SET RCP LABEL (for exported map legend) ----------------------------------
rcp_legend <- reactive({
if (!is.null(rcp())) {
if (rcp() == paste0("rcp45_", suffix())) {
"RCP4.5"
} else {
"RCP8.5"
}
} else {
NULL
}
})
### GET SELECTED INFORMATION (adapt depending on time period) ----------------
information <- reactive({
if (suffix() %in% c("climate", "species", "ecosystem", "network", "vulnerability")) {
if (suffix() == "species") {
if (period() != "1981-2010" && input[[paste0("infos_", suffix())]] == paste0("observations_", suffix())){
paste0("binaries_", suffix())
} else {
input[[paste0("infos_", suffix())]]
}
} else {
if (suffix() == "climate") {
if (period() == "1981-2010"){
paste0("normals_", suffix())
} else {
input[[paste0("infos_", suffix())]]
}
} else {
if (suffix() == "ecosystem") {
if (period() == "1981-2010"){
"richness"
} else {
input[[paste0("infos_", suffix())]]
}
} else {
if (suffix() == "network") {
if (period() == "1981-2010"){
paste0("values_", suffix())
} else {
input[[paste0("infos_", suffix())]]
}
} else {
"vulnerability"
}
}
}
}
} else {
NULL
}
})
### DEFINE LEAFLET LEGEND TITLE ----------------------------------------------
leaflet_title <- reactive({
if (!is.null(var_selected())) {
if (suffix() == "climate") {
if (information() == paste0("normals_", suffix())) {
"Climate normals"
} else {
if (information() == paste0("uncertainties_", suffix())) {
"Uncertainties"
} else {
"Anomalies"
}
}
} else {
if (suffix() == "species") {
if (information() == paste0("observations_", suffix())) {
"Observations"
} else {
if (information() == paste0("binaries_", suffix())) {
"Presence/absence"
} else {
if (information() == paste0("probabilities_", suffix())) {
"Probabilities"
} else {
"Uncertainties"
}
}
}
} else {
if (suffix() == "ecosystem") {
if (information() == "richness") {
if (spclass() == "total") {
"Number of species"
} else {
if (spclass() == "birds") {
"Number of species<br />(birds)"
} else {
"Number of species<br />(mammals)"
}
}
} else {
if (information() == "gains") {
if (spclass() == "total") {
"Species gains (%)"
} else {
if (spclass() == "birds") {
"Species gains (%)<br />(birds)"
} else {
"Species gains (%)<br />(mammals)"
}
}
} else {
if (information() == "losses") {
if (spclass() == "total") {
"Species losses (%)"
} else {
if (spclass() == "birds") {
"Species losses (%)<br />(birds)"
} else {
"Species losses (%)<br />(birds)"
}
}
} else {
if (spclass() == "total") {
"Total turnover"
} else {
if (spclass() == "birds") {
"Birds turnover"
} else {
"Mammals turnover"
}
}
}
}
}
} else {
if (suffix() == "network") {
if (information() == paste0("values_", suffix())) {
"Values"
} else {
"Anomalies"
}
} else {
"Vulnerability index"
}
}
}
}
} else {
NULL
}
})
### DEFINE VARIABLE NAME (for exported map) ----------------------------------
var_english <- reactive({
if (!is.null(var_selected())) {
if (suffix() %in% c("climate", "species", "network", "vulnerability")) {
pos <- NULL
for (i in columns()) {
if (length(which(data()[ , i] == var_selected())) == 1) {
pos <- which(data()[ , i] == var_selected())
}
}
as.character(data()[pos, grep("^english$|^common_en$", colnames(data()))])
} else {
pos <- which(data()[ , "info"] == information() & data()[ , "class"] == spclass())
xxx <- data()[pos, "english"]
if (length(grep(" \\(%\\)", xxx)) == 1) {
xxx <- paste0("Percentage of ", gsub(" \\(%\\)", "", xxx))
xxx <- gsub("S", "s", xxx)
}
paste0(xxx, " (", data()[pos, "class"], ")")
}
} else {
NULL
}
})
### DEFINE LEGEND TITLE (for exported map) -----------------------------------
legend_title <- reactive({
if (!is.null(var_selected())) {
if (suffix() == "climate") {
if (information() == paste0("normals_", suffix())) {
leg_suffix <- ""
} else {
if (information() == paste0("uncertainties_", suffix())) {
leg_suffix <- " (Uncertainties)"
} else {
leg_suffix <- " (Anomalies)"
}
}
} else {
if (suffix() == "species") {
if (information() == paste0("observations_", suffix())) {
leg_suffix <- " (Observations)"
} else {
if (information() == paste0("binaries_", suffix())) {
leg_suffix <- ""
} else {
if (information() == paste0("probabilities_", suffix())) {
leg_suffix <- ""
} else {
leg_suffix <- " (Uncertainties)"
}
}
}
} else {
if (suffix() == "network") {
if (information() == paste0("anomalies_", suffix())) {
leg_suffix <- " (Anomalies)"
} else {
leg_suffix <- ""
}
} else {
leg_suffix <- ""
}
}
}
paste0(
var_english(),
ifelse(
test = !is.null(var_units()),
yes = paste0(" (in ", var_units(), ") "),
no = " "
),
period(),
ifelse(
!is.null(rcp()),
paste0(" [", rcp_legend(), "]"),
""
),
leg_suffix
)
} else {
NULL
}
})
### DATA SOURCE (for exported map) -------------------------------------------
data_source <- reactive({
if (!is.null(var_selected())) {
if (suffix() == "species") {
if (information() == "observations_species") {
if (spclass() == "Aves") {
datasource <- "BirdLife International & NatureServe"
} else {
datasource <- "IUCN"
}
} else {
datasource <- NULL
}
} else {
if (suffix() == "climate") {
if (period() == "1981-2010") {
datasource <- "NCEP-CFSR Reanalysis"
} else {
datasource <- "CORDEX/Ouranos"
}
} else {
NULL
}
}
} else {
NULL
}
})
### GET FILENAME SUFFIX (if required) ----------------------------------------
filename_ext <- reactive({
if (!is.null(var_selected())) {
if (suffix() == "climate") {
if (information() == paste0("normals_", suffix())) {
"_mean"
} else {
if (information() == paste0("uncertainties_", suffix())) {
"_sd"
} else {
"_diff"
}
}
} else {
if (suffix() == "species") {
if (information() == paste0("observations_", suffix())) {
"_observations"
} else {
if (information() == paste0("binaries_", suffix())) {
"_binaries"
} else {
if (information() == paste0("probabilities_", suffix())) {
"_probabilities"
} else {
"_uncertainties"
}
}
}
} else {
if (suffix() == "network") {
if (information() == paste0("anomalies_", suffix())) {
"_diff"
} else {
""
}
} else {
""
}
}
}
} else {
NULL
}
})
### SET RASTER PATH ------------------------------------------------------
raster_path <- reactive({
if (!is.null(var_selected())) {
if (suffix() %in% c("climate", "species", "network", "vulnerability")) {
pos <- NULL
for (i in columns()) {
if (length(which(data()[ , i] == var_selected())) == 1) {
pos <- which(data()[ , i] == var_selected())
}
}
} else {
pos <- which(data()[ , "info"] == information() & data()[ , "class"] == spclass())
}
code <- data()[pos, "code"]
if (period() == "1981-2010"){
paste0(
"data/",