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app.R
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library(tidyverse)
library(readxl)
library(shiny)
library(shinydashboard)
library(rgdal)
library(leaflet)
library(lubridate)
if(!require(shinythemes)) install.packages("shinythemes")
if(!require(geojsonio)) install.packages("geojsonio")
library(htmltools)
library(DT)
library(lubridate)
library(mapview)
library(foreign)
library(webshot)
webshot::install_phantomjs()
source("LoadAlerts.R")
# LOAD DATA
# ---------------------
# STEP 1 - LOAD ALERTS INTO A DATAFRAME
# 1.1 Raw Data
options(DT.options = list(language=list("https://cdn.datatables.net/plug-ins/1.10.21/i18n/French.json"),
buttons = list()))
current_date <- Sys.Date()
pcodes_adm3 <- read_csv("INPUT/DATA/PCodes/MLI_PCodesAdmin3.csv")
pcodes_adm2 <- pcodes_adm3%>%
select(Admin1_Nam,Pcode_Ad_1,Admin2_Nam,Pcode_Ad_2)%>%
distinct()
pcodes_adm1<- pcodes_adm3%>%
select(Admin1_Nam,Pcode_Ad_1)%>%
distinct()
# 1.2 Base Map
mli_adm2_shp <- readOGR("INPUT/Shapes/mli_adm2_withMenaka.shp")
mli_adm1_shp <- readOGR("INPUT/Shapes/mli_adm1_withMenaka.shp")
bins_adm2 <- c(0,1000,5000,10000,20000, Inf)
bins_adm1 <- c(0,10000,30000,50000,100000, Inf)
REACH_colors <- colorRamp(c("#FCE3E4","#FAD3D4", "#F8BABB", "#F6A9AA","#F49495","#EE5859"))
# basemap <- leaflet(mli_adm2_shp)%>%
# addProviderTiles(providers$Esri.WorldGrayCanvas) %>%
# addPolygons(weight = 1, stroke = F)
### SHINY DASHBOARD
ui <- bootstrapPage(
navbarPage(collapsible = TRUE,
theme = shinytheme("flatly"),
title ="RRM - Mali", id="nav",
tabPanel("Alertes", id = "cercles",
div(class = "outer",
tags$head(includeCSS("style.css")),
leafletOutput(paste0("mymap"), width="100%", height="60%"),
absolutePanel(id = "controls", class = "panel panel-default",
top = 75, left = 70, width = 300, fixed=TRUE,
draggable = FALSE, height = "auto",
radioButtons("adm_level", h5("Niveau administratif d'accueil"),
choices = c("Cercles" = "cercles", "Régions" = "regions")),
dateRangeInput("plot_date",
label = h5("Dates"),
start = as.Date("2018-01-01","%Y-%m-%d"),
end = as.Date(current_date,"%Y-%m-%d"),
format = "dd.mm.yyyy",
language = "fr",
weekstart =1
),
fileInput("datafile", "Charger données", accept = c("application/vnd.ms-excel",
"application/vnd.ms-excel.sheet.macroenabled.12",
"text/csv",
".xlsx",
".xlsm")),
downloadButton("dl", "Télécharger carte")
),
dataTableOutput("alertsTable")
)
)
)
)
server <- function(input, output, session){
Sys.setlocale("LC_ALL", "fr_FR")
Alerts <- reactive({
req(input$datafile)
inFile <- input$datafile
dataPath <- inFile$datapath
loadAlerts(dataPath = dataPath, pcodes_adm2 = pcodes_adm2)
})
basemap <- reactive({
leaflet(mli_adm2_shp)%>%
addProviderTiles(providers$Esri.WorldGrayCanvas) %>%
addPolygons(weight = 1, stroke = F, color = "grey")
})
options(DT.options = list(language=list(url="https://cdn.datatables.net/plug-ins/1.10.21/i18n/French.json")))
reactive_db_adm2 <- reactive({
req(Alerts)
db <- Alerts() %>%
filter(Date_evenement >= input$plot_date[1] & Date_evenement <= input$plot_date[2])%>%
group_by(Pcode_Ad_2)%>%
summarise(sum_HH = sum(Effectifs_Estimatif_des_menages, na.rm = T), nb_alerts = n())%>%
ungroup()
names(db) <- c("Pcode_Ad_2", "sum_HH", "nb_alerts")
db
})
reactive_polygons_adm2 <- reactive({
mli_adm2_shp[mli_adm2_shp$admin2Pcod %in% reactive_db_adm2()$Pcode_Ad_2, ]%>%
sp::merge(as.data.frame(reactive_db_adm2()), by.x ="admin2Pcod", by.y = "Pcode_Ad_2")
})
output$mymap <- renderLeaflet({
basemap()
})
reactive_db_adm1 <- reactive({
req(Alerts)
db <- Alerts() %>%
filter(Date_evenement >= input$plot_date[1] & Date_evenement <= input$plot_date[2])%>%
group_by(Pcode_Ad_1)%>%
summarise(sum_HH = sum(Effectifs_Estimatif_des_menages, na.rm = T), nb_alerts = n())%>%
ungroup()
names(db) <- c("Pcode_Ad_1", "sum_HH", "nb_alerts")
db
})
reactive_polygons_adm1 <- reactive({
mli_adm1_shp[mli_adm1_shp$admin1Pcod %in% reactive_db_adm1()$Pcode_Ad_1, ]%>%
sp::merge(as.data.frame(reactive_db_adm1()), by.x ="admin1Pcod", by.y = "Pcode_Ad_1")
})
observe({
rrm_pal_adm2 <- colorBin(REACH_colors, domain = Alerts()$Effectifs_Estimatif_des_menages, bins = bins_adm2)
rrm_pal_adm1 <- colorBin(REACH_colors, domain = Alerts()$Effectifs_Estimatif_des_menages, bins = bins_adm1)
req(Alerts)
if(input$adm_level == "cercles"){
leafletProxy("mymap")%>%
clearControls()%>%
clearMarkers() %>%
clearShapes() %>%
addCircles(data = reactive_polygons_adm2(),
lat = coordinates(reactive_polygons_adm2())[,2],
lng = coordinates(reactive_polygons_adm2())[,1],
radius = reactive_polygons_adm2()$sum_HH*5,
stroke = T, color = "#red", weight = 3, fillColor = "red", fillOpacity = 0.9,
label = mapply(function(x, y,z) {
HTML(sprintf("<div><b>%s </b> </div>
<div>Ménages déplacés (alerte): %s</div>
<div>Nombre d'alertes: %s </div>", htmlEscape(x), htmlEscape(y),htmlEscape(z)
))},
reactive_polygons_adm2()$admin2Name, reactive_polygons_adm2()$sum_HH,reactive_polygons_adm2()$nb_alerts,
SIMPLIFY = F),
labelOptions = labelOptions(noHide = F),
opacity = 0.9
)
# addPolygons(data = reactive_polygons_adm2(),
# stroke = T, color = "white", weight = 1,
# # label = mapply(function(x, y,z) {
# # HTML(sprintf("<div><b>%s </b> </div>
# # <div>Ménages déplacés (alerte): %s</div>
# # <div>Nombre d'alertes: %s </div>", htmlEscape(x), htmlEscape(y),htmlEscape(z)
# # ))},
# # reactive_polygons_adm2()$admin2Name, reactive_polygons_adm2()$sum_HH,reactive_polygons_adm2()$nb_alerts,
# # SIMPLIFY = F),
# # labelOptions = labelOptions(noHide = F),
# fillColor = "grey",
# fillOpacity = 0.1,
# )%>%
# addLegend("bottomright", pal = rrm_pal_adm2, values = Alerts()$Effectifs_Estimatif_des_menages,
# title = "Nombre de ménages recensés lors des alertes")
}
if(input$adm_level == "regions"){
leafletProxy("mymap")%>%
clearControls()%>%
clearMarkers() %>%
clearShapes() %>%
addPolygons(data = reactive_polygons_adm1(),
stroke = T, color = "White", weight = 2,
label = mapply(function(x, y,z) {
HTML(sprintf("<div><b>%s </b> </div>
<div>Ménages déplacés (alerte): %s</div>
<div>Nombre d'alertes: %s </div>", htmlEscape(x), htmlEscape(y),htmlEscape(z)
))},
reactive_polygons_adm1()$admin1Name, reactive_polygons_adm1()$sum_HH,reactive_polygons_adm1()$nb_alerts, SIMPLIFY = F),
labelOptions = labelOptions(noHide = F),
fillColor = ~rrm_pal_adm1(reactive_polygons_adm1()$sum_HH),
fillOpacity = 0.9
)%>%
addLegend("bottomright", pal = rrm_pal_adm1, values = Alerts()$Effectifs_Estimatif_des_menages,
title = "Nombre de ménages recensés lors des alertes")
}
})
reactive_alerts <- reactiveValues(alerts = NULL)
observe({
req(Alerts)
if(input$adm_level == "cercles"){
reactive_alerts$alerts<-Alerts() %>%
filter(Date_evenement >= input$plot_date[1] & Date_evenement <= input$plot_date[2])%>%
group_by(Pcode_Ad_2)%>%
summarise(sum_HH = sum(Effectifs_Estimatif_des_menages, na.rm = T), nb_alerts = n())%>%
ungroup()%>%
left_join(pcodes_adm2, by= "Pcode_Ad_2")%>%
select(Admin1_Nam,Admin2_Nam, sum_HH, nb_alerts, Pcode_Ad_1,Pcode_Ad_2)%>%
rename("Région d'accueil" = Admin1_Nam,
"Cercle d'accueil" = Admin2_Nam,
"Ménages affectés" = sum_HH,
"Nombre Alertes" = nb_alerts,
"PCode Région" = Pcode_Ad_1,
"PCode Cercle" = Pcode_Ad_2
)%>%
datatable( options = list(dom = 'Bfrtip', autoWidth = TRUE, scrollY ="25vh", paging = FALSE,
buttons = list(list(extend='copy', text ="Copier"),
list(extend = 'csv', filename = paste0("RRM-Mali_",input$adm_level,"_",input$plot_date[1]," - ",input$plot_date[2])),
list(extend = 'excel', filename = paste0("RRM-Mali_",input$adm_level,"_",input$plot_date[1]," - ",input$plot_date[2]))
)
),
class = "compact", extensions=c("Buttons"), rownames= FALSE)
}
if(input$adm_level == "regions"){
reactive_alerts$alerts <- Alerts() %>%
filter(Date_evenement >= input$plot_date[1] & Date_evenement <= input$plot_date[2])%>%
group_by(Pcode_Ad_1)%>%
summarise(sum_HH = sum(Effectifs_Estimatif_des_menages, na.rm = T), nb_alerts = n())%>%
ungroup()%>%
left_join(pcodes_adm1, by= "Pcode_Ad_1")%>%
select(Admin1_Nam, sum_HH, nb_alerts, Pcode_Ad_1)%>%
rename("Région d'accueil" = Admin1_Nam,
"Ménages affectés" = sum_HH,
"Nombre Alertes" = nb_alerts,
"PCode Région" = Pcode_Ad_1,
)%>%
datatable(callback=JS('$(".buttons-csv").css("background","red");
$("a.buttons-print").css("background","green");
return table;'),
options = list(dom = 'Bfrtip', autoWidth = TRUE, scrollY ="25vh", paging = FALSE,
buttons = list(list(extend = 'copy', text ="Copier"),
list(extend = 'csv', filename = paste0("RRM-Mali_",input$adm_level,"_",input$plot_date[1]," - ",input$plot_date[2])),
list(extend = 'excel', filename = paste0("RRM-Mali_",input$adm_level,"_",input$plot_date[1]," - ",input$plot_date[2]))
)
),
class = "compact", extensions=c("Buttons"), rownames= FALSE,
)
}
})
output$alertsTable <- renderDataTable(reactive_alerts$alerts, server = FALSE)
user_created_map <- reactive({
rrm_pal_adm2 <- colorBin(REACH_colors, domain = Alerts()$Effectifs_Estimatif_des_menages, bins = bins_adm2)
rrm_pal_adm1 <- colorBin(REACH_colors, domain = Alerts()$Effectifs_Estimatif_des_menages, bins = bins_adm1)
m <- basemap()
title <- paste0("RRM-Mali - Carte par ",input$adm_level,": ",format(as.Date(input$plot_date[1], "%Y-%m-%d"),"%d %B %Y"), ""," - ",format(as.Date(input$plot_date[2],"%Y-%m-%d"), "%d %B %Y"))
if(input$adm_level == "cercles"){
m <- m%>%
addCircles(data = reactive_polygons_adm2(), stroke=T, radius = reactive_polygons_adm1()$nb_alerts, color = "#FCE3E4")%>%
addPolygons(data = reactive_polygons_adm2(),
stroke = T, color = "White", weight = 2,
label = mapply(function(x, y,z) {
HTML(sprintf("<div><b>%s </b> </div>
<div>Ménages déplacés (alerte): %s</div>
<div>Nombre d'alertes: %s </div>", htmlEscape(x), htmlEscape(y),htmlEscape(z)
))},
reactive_polygons_adm2()$admin2Name, reactive_polygons_adm2()$sum_HH,reactive_polygons_adm2()$nb_alerts,
SIMPLIFY = F),
labelOptions = labelOptions(noHide = F),
fillColor = ~rrm_pal_adm2(reactive_polygons_adm2()$sum_HH),
fillOpacity = 0.9
)%>%
addLegend("bottomright", pal = rrm_pal_adm2, values = Alerts()$Effectifs_Estimatif_des_menages,
title = "Nombre de ménages recensés lors des alertes")%>%
addControl(title, position = "topleft")
}
if(input$adm_level == "regions"){
m <- m%>%
addPolygons(data = reactive_polygons_adm1(),
stroke = T, color = "White", weight = 2,
label = mapply(function(x, y,z) {
HTML(sprintf("<div><b>%s </b> </div>
<div>Ménages déplacés (alerte): %s</div>
<div>Nombre d'alertes: %s </div>", htmlEscape(x), htmlEscape(y),htmlEscape(z)
))},
reactive_polygons_adm1()$admin1Name, reactive_polygons_adm1()$sum_HH,reactive_polygons_adm1()$nb_alerts, SIMPLIFY = F),
labelOptions = labelOptions(noHide = F),
fillColor = ~rrm_pal_adm1(reactive_polygons_adm1()$sum_HH),
fillOpacity = 0.9
)%>%
addLegend("bottomright", pal = rrm_pal_adm1, values = Alerts()$Effectifs_Estimatif_des_menages,
title = "Nombre de ménages recensés lors des alertes")%>%
addControl()
}
m
})
output$dl <- downloadHandler(
filename <- function(){
paste0("/RRM-Mali_",input$adm_level,"_",input$plot_date[1]," - ",input$plot_date[2], ".png")
},
content = function(file) {
mapshot(user_created_map(), file=file)
}
)
}
shinyApp(ui, server)