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app.R
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#Load libraries
library(gdm)
library(leaflet)
library(raster)
library(rgdal)
library(rgeos)
library(shiny)
library(shinycssloaders)
library(shinyjs)
library(png)
#Load functions
source("FindNextLight2.R")
source("MapGDMLight.R")
source("extractMainVeg2.R")
source("helpers.R")
source("Misc.R")
source("rgbPalette.R")
# Load app data
load("appData/occ.table2.RData")
load("appData/gdm.ebird.all.RData") #ebird.all ~ gbd2017
load("appData/gdm.raster.ebird.all.RData") #ebird.all ~ gbd2017
load('appData/col_runap.RData')
load("appData/results.RData")
env.data<-stack("./appData/env.data5.utm.grd")
env.data.coarse<-stack("./appData/env.data20.utm.grd")
dem.data <- raster("./appData/dem_utm.tif")
vias <- raster("./appData/distFromRoadsRivers.tif")
col@data$DEPARTAMEN <- as.character(col@data$DEPARTAMEN)
occ.coords<-data.frame(getLatLon(occ.table[,c("lon","lat")], projection(env.data)))
ui <- fluidPage(
# Call font
tags$link(
rel = "stylesheet",
href="https://fonts.googleapis.com/css?family=Raleway:400,400i|Roboto:300,300i,400,400i,700,700i"
),
#tags$style("h2{font-family: 'Open Sans'}"),
## Call css
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "chapman.css")
),
tags$head(includeHTML(("muestreo-analytics.html"))),
useShinyjs(),
inlineCSS(appCSS),
titlePanel("Chapman: Sistema de recomendación de muestreo"),
sidebarLayout(
sidebarPanel(
h4(HTML("<b>Seleccione área de interés:<b>")),
selectInput("aoi", label=NULL, width = '70%',
choices = c('COLOMBIA', sort(unique(col@data$DEPARTAMEN)))),
actionButton(inputId ="see", label="Ver Resultados",class="btn-primary"),
br(),br(),
withBusyIndicatorUI(
actionButton(inputId ="go", label="Personalizar (beta)",class="btn-primary")
),
br(),
h4(HTML("<b>Descargar:<b>")),
radioButtons("resultType",label="Escoja resultado",
choices=c("Precalculado","Personalizado"),
selected="Precalculado"),
h5(HTML("<b> a. Capa de puntos:<b>")),
downloadButton('dwnShape', 'Puntos (.shp)'),
h5(HTML("<b> b. Raster:<b>")),
downloadButton('dwnRaster', 'Raster (.tif)'),
h5(HTML("<b> c. Tabla localidades:<b>")),
downloadButton('dwnTable', 'Localidades (.csv)'),
br(),
br(),
br(),
img(src = "humboldt-01.png", height = 87, width = 80),
img(src = "Logo_GBD_Final-01.png", height = 108, width = 241)
),
mainPanel(
tabsetPanel(id = "inTabset",
tabPanel('Inicio', includeMarkdown("introMD.md")),
tabPanel('Acerca de', includeMarkdown("aboutMD.md")),
tabPanel('Resultados',
fluidRow(withSpinner(leafletOutput("resultMap", width = "100%", height = 500),
type = 1)),
img(src = "legend.png", height = 50.7, width = 303),
br(),
fluidRow(tableOutput("resultTable"))
),
tabPanel('Personalizar',
fluidRow(
h5(HTML("<b>Busque el sitio más complementario:<b>")),
column(width = 2, withBusyIndicatorUI(actionButton(inputId = "findNext", label=" Sugerir", icon =icon('angle-up')))),
column(width = 2, actionButton(inputId = "ignoreSite",label=" Descartar", icon =icon('angle-down'))),
column(width = 1, h6(HTML("Latitud"))),
column(width = 2, textInput(inputId="lat", label = NULL, width = '200px', value=0)),
column(width = 1, h6(HTML("Longitud"))),
column(width = 2, textInput(inputId="lon", label = NULL, width = '200px', value=0)),
column(width = 1, actionButton(inputId = "goMap", label="Añadir"))
),
fluidRow(withSpinner(plotOutput("nicemap", width = "100%", height = 500),
type = 1)),
radioButtons("mapType", label="Mostrar:", choices=c("Comunidades","Complementariedad"), selected="Comunidades", inline=T),
br(), br(),
fluidRow(tableOutput("table1")))
)
)
)
)
server <- function(input, output, session) {
disable(id = "findNext", selector = NULL)
disable(id = "ignoreSite", selector = NULL)
disable(id = "addCustomSite", selector = NULL)
disable(id = "lat", selector = NULL)
disable(id = "lon", selector = NULL)
disable(id = "goMap", selector = NULL)
rv <- reactiveValues()
observeEvent(input$go,{
withBusyIndicatorServer("go",{
updateTabsetPanel(session, "inTabset", selected = "Personalizar")
rv$aoi<-NULL
rv$gdm.raster<-NULL
rv$env.data.aoi<-NULL
rv$out.table <- NULL
rv$dist.raster <- NULL
## Disable Buttoms
disable(id = "findNext", selector = NULL)
disable(id = "ignoreSite", selector = NULL)
disable(id = "addCustomSite", selector = NULL)
disable(id = "lat", selector = NULL)
disable(id = "lon", selector = NULL)
if(input$aoi=="COLOMBIA"){
rv$env.data.aoi <- env.data.coarse
rv$aoi <- env.data.coarse[[1]]
} else {
rv$aoi <- col[col@data$DEPARTAMEN==input$aoi, ]
rv$env.data.aoi <- env.data
}
rv$gdm.raster <- results[[input$aoi]]$gdm.col.aoi
enable(id = "findNext", selector = NULL)
enable(id = "ignoreSite", selector = NULL)
enable(id = "goMap", selector = NULL)
enable(id = "lat", selector = NULL)
enable(id = "lon", selector = NULL)
})
})
observeEvent(input$see,{
withBusyIndicatorServer("go",{
updateTabsetPanel(session, "inTabset", selected = "Resultados")
})
})
observeEvent(input$findNext,{withBusyIndicatorServer("findNext",{
if(!is.null(rv$out.table)){
res <- FindNextLight2(gdm.rast, occ.table, rv$env.data.aoi, rv$aoi,
add.site=rv$out.table[, 1:2])
rv$out.table <- rbind(rv$out.table, res$dist.table[1, ])
rv$dist.raster <- res$dist.raster
} else {
res <- FindNextLight2(gdm.rast, occ.table, rv$env.data.aoi, rv$aoi,
add.site=NULL)
rv$out.table <- res$dist.table[1, ]
rv$dist.raster <- res$dist.raster
}
})
})
observeEvent(input$ignoreSite, {
ignore.cell<-cellFromXY(rv$env.data.aoi[[1]], rv$out.table[nrow(rv$out.table), 1:2])
rv$env.data.aoi[ignore.cell] <- NA
rv$gdm.raster[ignore.cell] <- NA
if(nrow(rv$out.table)==1){
rv$out.table <- NULL
} else {
rv$out.table <- rv$out.table[1:(nrow(rv$out.table)-1), ]
}
})
observeEvent(input$goMap,{
addRow <- data.frame(getUTMcoords(
data.frame(x=as.numeric(input$lon),
y=as.numeric(input$lat))), dist=NA)
rv$out.table <- rbind(rv$out.table, addRow)
})
#Plot precalculated results in Leaflet
output$resultMap <- renderLeaflet({
comRaster<-results[[input$aoi]]$gdm.col.aoi
if(input$aoi=="COLOMBIA"){
radSize<-14142.14
} else {
radSize<-3535.534
}
suggested<-results[[input$aoi]]$table1
bounds<-getLatLon(data.frame(lon=c(extent(comRaster)@xmin,extent(comRaster)@xmax),
lat=c(extent(comRaster)@ymin,extent(comRaster)@ymax)),
projection(comRaster))
niceLeaf <- leaflet(comRaster[[1]]) %>%
addTiles(group = 'Mapa base') %>%
addProviderTiles("Esri.WorldImagery",group="Satélite") %>%
addRasterImage(comRaster[[1]], colors = rgbPalette(comRaster), opacity =0.8, group = "Comunidades") %>%
addLayersControl(baseGroups=c("Mapa base","Satélite"),overlayGroups = c("Comunidades", "Muestreado","Sugerido", "Área sugerida"),
options = layersControlOptions(collapsed = FALSE)) %>%
fitBounds(lng1=min(bounds[,1]),
lng2=max(bounds[,1]),
lat1=min(bounds[,2]),
lat2=max(bounds[,2])) %>%
addCircleMarkers(lng = ~lon, lat = ~lat, data = occ.coords, group = "Muestreado", color= "#333333",
fillColor = '#fcf9d5', fillOpacity = 1, weight = 0.5, radius = 5,
label = occ.table$locality) %>%
addMarkers(lng = ~Longitud, lat = ~Latitud, data = suggested,
group = "Sugerido", label = paste0("Sitio: ",suggested$Sitio))%>%
addCircles(lng = ~Longitud, lat = ~Latitud, data = suggested,
group = "Área sugerida", radius=radSize, fillColor="dodgerblue", fillOpacity=0.6,weight=0,
label = paste0("Sitio: ",suggested$Sitio))
niceLeaf
})
#Plot interactive map using regular plotRGB function
output$nicemap <- renderPlot({
if(input$mapType=="Comunidades"){
if(!is.null(rv$gdm.raster)){
plotRGB(rv$gdm.raster)
if(input$aoi!="COLOMBIA"){
plot(rv$aoi,add=T,border="grey20")
}
points(occ.table[,3:2],pch=21,col="grey10",bg="#fcf9d5",cex=1.2)
if(!is.null(rv$out.table)){
points(rv$out.table,pch=25,col="grey10",bg="cyan",cex=2)
legend("bottomright",c("Sitios muestreados","Sitios sugeridos"),
col=c("grey10","grey10"),
pt.bg=c("#fcf9d5","cyan"),
pch=c(21,25),
bg="white",
bty="n")
} else {
legend("bottomright",c("Sitios muestreados"),
col=c("grey10"),
pt.bg=c("#fcf9d5"),
pch=c(21),
bg="white",
bty="n")
}
}
}
if(input$mapType=="Complementariedad"){
if(!is.null(rv$dist.raster)){
plot(rv$dist.raster,ext=rv$gdm.raster,col=colorRampPalette(c("forestgreen","yellow","red"))(255))
plot(rv$aoi,add=T,border="grey20")
points(occ.table[,3:2],pch=21,col="grey10",bg="#fcf9d5",cex=1.2)
if(!is.null(rv$out.table)){
points(rv$out.table,pch=25,col="grey10",bg="cyan",cex=2)
legend("bottomright",c("Sitios muestreados","Sitios sugeridos"),
col=c("grey10","grey10"),
pt.bg=c("#fcf9d5","cyan"),
pch=c(21,25),
bg="white",bty="n")
} else {
legend("bottomright",c("Sitios muestreados"),
col=c("grey10"),
pt.bg=c("#fcf9d5"),
pch=c(21),
bg="white")
}
}
}
})
#This is the table for interactive results
output$table1<-renderTable({
if(!is.null(rv$out.table)){
coords<-getLatLon(rv$out.table[,1:2],projection(env.data))
res2<<-data.frame(
Sitio=1:nrow(rv$out.table),
Latitud=coords[,2],
Longitud=coords[,1],
Elevación=extract(dem.data, rv$out.table[, 1:2]),
Municipio=extract(col, rv$out.table[, 1:2])$NOMBRE_ENT,
RUNAP=extract(runap, rv$out.table[, 1:2])$nombre,
CercaniaViasKm=extract(vias, rv$out.table[, 1:2])/1000,
Coberturas=extractMainVeg2(rv$out.table[, 1:2],env.data[[8:20]]),
ED_Total=rv$out.table[,3])
res3 <<- cbind(res2, coords)
res2
}
})
#This is the table for precalculated results
output$resultTable<-renderTable({
results[[input$aoi]]$table1
})
output$dwnTable <- downloadHandler(
filename = 'samplingSuggestions.csv',
content = function(filename) {
if(input$resultType=="Personalizado"){
write.csv(res3, filename, row.names = F, fileEncoding = "UTF-8")
}
if(input$resultType=="Precalculado"){
write.csv(results[[input$aoi]]$table1, filename, row.names = F, fileEncoding = "UTF-8")
}
})
output$dwnShape <- downloadHandler(
filename = 'samplingSuggestions.zip',
content = function(filename) {
if(input$resultType=="Precalculado"){
c.cols <- results[[input$aoi]]$table1[, c('Sitio','Latitud', 'Longitud')]
coordinates(c.cols) =~ Longitud+Latitud
c.cols@proj4string@projargs <- '+proj=longlat +ellps=WGS84 +towgs84=0,0,0,0,0,0,0 +no_defs'
c.cols@data <- results[[input$aoi]]$table1
}
if(input$resultType=="Personalizado"){
c.cols <- res2[, c('Sitio','Latitud', 'Longitud')]
coordinates(c.cols) =~ Longitud+Latitud
c.cols@proj4string@projargs <- '+proj=longlat +ellps=WGS84 +towgs84=0,0,0,0,0,0,0 +no_defs'
c.cols@data <- res2
}
writeZip(c.cols, filename, .file = 'Sitios_muestreo')
})
output$dwnRaster <- downloadHandler(
filename = 'gdmRaster.tif',
content = function(filename) {
outRaster<-results[[input$aoi]]$gdm.col.aoi
outRaster<-projectRaster(outRaster,crs='+proj=longlat +ellps=WGS84 +towgs84=0,0,0,0,0,0,0 +no_defs')
writeRaster(outRaster, filename=filename, options="INTERLEAVE=BAND", format="GTiff", overwrite=TRUE)
})
}
shinyApp(ui = ui, server = server)