In juldebar/IRDTunaAtlas: IRD (www.ird.fr) - UMR EME - Tuna atlas

library(flexdashboard)
library(shiny)
library(dplyr)
library(XML)
library(DBI)
library(RPostgres)
library(RPostgreSQL)
library(dplyr)
library(leaflet)
library(leaflet.extras)
library(leafpm)
library(mapedit)
library(sf)
library(sp)
library(plotly)
library(ggplot2)
library(plyr)

#######################
##Database Identifiers:
DRV=RPostgres::Postgres()
source(file = "~/Desktop/CODES/IRDTunaAtlas/credentials.R")
####################################################################################################################################################################################################################################
source("https://raw.githubusercontent.com/juldebar/IRDTunaAtlas/master/R/TunaAtlas_i6_SpeciesMap.R")
source("https://raw.githubusercontent.com/juldebar/IRDTunaAtlas/master/R/TunaAtlas_i7_SpeciesMapRelativeCatches.R")
source("https://raw.githubusercontent.com/juldebar/IRDTunaAtlas/master/R/TunaAtlas_i8_SpeciesMapRelativeCatchesOtherSpecies.R")

## server side code
function(input, output, session) {
  output$table <- DT::renderDataTable({
    # query <- sqlInterpolate(ANSI(),"SELECT ogc_fid, geom_id, geom, year, species, country, value, count FROM i6i7i8 WHERE species IN ('?species') AND year IN ('?year');",
    #             species =paste0(input$year_choice_i6i7,collapse="','"), year = paste0(input$year_choice_i6i7,collapse="','"))

    df_i6i7 = st_read(con, 
                      query =  paste0("SELECT ogc_fid, geom_id, geom, year, species, country, value, count FROM public.i6i7i8 WHERE ST_Within(geom,ST_GeomFromText('",wkt(),"',4326)) AND species IN ('",paste0(input$species_i6i7i8,collapse="','"),"') AND year IN ('",paste0(input$year_choice_i6i7,collapse="','"),"');")
                      )

    outp <- dbGetQuery(pool, query)
    ret <- DT::datatable(outp)
    return(ret)
  })
}

Column {data-width=350}

Select parameters to customize plots 1, 2, 3 and 4 (see Github wiki)

# Check http://jeffgoldsmith.com/p8105_f2017/shiny.html

new_wkt <- 'POLYGON((-180 -90, 180 -90, 180 90, -180 90, -180 -90))'
wkt <- reactiveVal(new_wkt) 
target_species_i8<- c("YFT","BET","SKJ")
target_species_i6i7<- c("YFT")
# target_year <- c(seq(1:10)+1994)
target_year<- c(2000)
target_year_i8 <- c(1999,2000)


query_i6i7i8 <- paste0("SELECT ogc_fid, geom_id, geom, year, species, country, value, count FROM i6i7i8 WHERE species IN ('",paste0(target_species_i8,collapse="','"),"') AND year IN ('",paste0(target_year,collapse="','"),"');")
df_i6i7i8 = st_read(con, query = query_i6i7i8)
year_i6i7i8 = unique(df_i6i7i8$year)
species_i6i7i8 = unique(df_i6i7i8$species)


# selectInput widget

selectInput("species_i6i7i8", label = h3("Select species for i8 (at least two species):"), choices = species_i6i7i8, selected = target_species_i8, multiple = TRUE)
selectInput("year_choice_i8", label = h3("Select year for i8 (if multiple years, generates one map per year):"), choices = year_i6i7i8, selected = target_year_i8,multiple = TRUE)

selectInput("species_i6i7i8", label = h3("Select species for  i6, i7"), choices = species_i6i7i8, selected = target_species_i6i7, multiple = FALSE)
selectInput("year_choice_i6i7", label = h3("Select year for  i6, i7"), choices = year_i6i7i8, selected = target_year, multiple = FALSE)


# textOutput(wkt())

renderPrint({ 
  paste0("The area you have selected is (WKT format): ", wkt())
  query_i6i7i8 <-  paste0("SELECT ogc_fid, geom_id, geom, year, species, country, value, count FROM public.i6i7i8 WHERE ST_Within(geom,ST_GeomFromText('",wkt(),"',4326)) AND species IN ('",paste0(input$species_i6i7i8,collapse="','"),"') AND year IN ('",paste0(input$year_choice_i8,collapse="','"),"');")

})

# renderDataTable(
#   
# )

Select WKT on the map

To be done : add all WMS layers of input datasets

output$mymap <- renderLeaflet(
leaflet() %>%
addTiles() %>%
# addPmToolbar(
#   toolbarOptions = pmToolbarOptions(drawMarker = FALSE, position = "topright"),
#   drawOptions = pmDrawOptions(snappable = FALSE, allowSelfIntersection = FALSE),
#   editOptions = pmEditOptions(preventMarkerRemoval = TRUE, draggable = FALSE),
#   cutOptions = pmCutOptions(snappable = FALSE, allowSelfIntersection = FALSE)
# ) %>%
    addDrawToolbar(
        targetGroup = "draw",
        editOptions = editToolbarOptions(
            selectedPathOptions = selectedPathOptions()
        )
    )   %>% setView(lng =48, lat =-8, zoom = 5
        ) %>% addWMSTiles(
    # "http://thredds.oreme.org:8080/thredds/wms/MARBEC/Seychelles/global-reanalysis-phy-001-030-monthly_SEY_t55_199301-201906.nc",
    "https://geoserver-sdi-lab.d4science.org/geoserver/sdilab_geoflow/ows?service=WMS",
    layers = "global_catch_5deg_1m_ird_level0",
        # layers = "thetao",
        options = WMSTileOptions(format = "image/png", transparent = TRUE), group ="Seatizen", attribution = "Seatizen WMS"
  )  %>%
    addLayersControl(
        overlayGroups = c("draw"),
        options = layersControlOptions(collapsed = FALSE)
    ) 

)
    leafletOutput('mymap')  


        observe({
              #use the draw_stop event to detect when users finished drawing
            feature <- input$mymap_draw_new_feature
            req(input$mymap_draw_stop)
            print(feature)
            polygon_coordinates <- input$mymap_draw_new_feature$geometry$coordinates[[1]]
            # see  https://rstudio.github.io/leaflet/shiny.html
            bb <- input$mymap_bounds 
            geom_polygon <- input$mymap_draw_new_feature$geometry
            # drawn_polygon <- Polygon(do.call(rbind,lapply(polygon_coordinates,function(x){c(x[[1]][1],x[[2]][1])})))
            geoJson <- geojsonio::as.json(feature)
            # spdf <- geojsonio::geojson_sp(feature)
            geom <- st_read(geoJson)
            wkt(st_as_text(st_geometry(geom[1,])))
            coord <- st_as_text(st_geometry(geom[1,]))

            north <- polygon_coordinates[[1]][[1]]
            south <- polygon_coordinates[[2]][[1]]
            east <- polygon_coordinates[[1]][[2]]
            west <- polygon_coordinates[[2]][[2]]


            if(is.null(polygon_coordinates))
                return()
            text<-paste("North ", north, "South ", east)

            mymap_proxy = leafletProxy("mymap") %>% clearPopups() %>% addPopups(south,west,coord)
            textOutput("wkt")

            if(wkt()!=new_wkt){
  df_i6i7i8 = st_read(con, 
                      query =  paste0("SELECT ogc_fid, geom_id, geom, year, species, country, value, count FROM public.i6i7i8 WHERE ST_Within(geom,ST_GeomFromText('",wkt(),"',4326)) AND species IN ('",paste0(input$species_i6i7i8,collapse="','"),"') AND year IN ('",paste0(input$year_choice_i6i7,collapse="','"),"');")
  )
            }

        })

Column {data-width=650}

Plot 8 IIndicator I8 : Catches relative contribution over other species

# https://plotly.com/r/maps-sf/
# https://ggplot2.tidyverse.org/reference/ggsf.html
output$plot8 <- renderPlotly({ 

if(wkt()!=new_wkt){
  df_i8 = st_read(con, 
                      query =  paste0("SELECT ogc_fid, geom_id, geom, year, species, country, value, count FROM public.i6i7i8 WHERE ST_Within(geom,ST_GeomFromText('",wkt(),"',4326)) AND species IN ('",paste0(input$species_i6i7i8,collapse="','"),"') AND year IN ('",paste0(input$year_choice_i8,collapse="','"),"');")
                  )
}else{
  df_i8=df_i6i7i8
}


# df_i6i7i8_filtered <- df_i6i7i8 %>% filter(year %in% target_year, species %in% target_species)
# df_i6i7i8_filtered <- df_i6i7i8 %>% filter(year %in% input$year_choice_i8, species %in% input$species_i6i7i8) 
df_i8_filtered <- as(df_i8, "Spatial")

i8 <- Atlas_i8_SpeciesMapRelativeCatchesOtherSpecies(df=df_i8_filtered,
                                             targetedSpecies=input$species_i6i7i8[1],
                                             geomIdAttributeName="geom_id",
                                             yearAttributeName="year",
                                             speciesAttributeName="species",
                                             valueAttributeName="value",
                          withSparql=FALSE
                          )

# i8 <-  plot_geo(df_i8_filtered)


})
plotlyOutput("plot8")

Plot 7 Indicator I7 : 5x5 degrees relative contribution to catches

output$plot7 <- renderPlotly({


  if(wkt()!=new_wkt){

    df_i6i7 = st_read(con, 
                      query =  paste0("SELECT ogc_fid, geom_id, geom, year, species, country, value, count FROM public.i6i7i8 WHERE ST_Within(geom,ST_GeomFromText('",wkt(),"',4326)) AND species IN ('",paste0(input$species_i6i7i8,collapse="','"),"') AND year IN ('",paste0(input$year_choice_i6i7,collapse="','"),"');")
                      )
}else{
  df_i6i7=df_i6i7i8
}


# df_i6i7i8_filtered <- df_i6i7i8 %>% filter(year %in% input$year_choice_i8, species %in% input$species_i6i7i8) 


#Filtering input dataset with selected parameters

# df_i6i7i8_filtered <- df_i6i7i8 %>% filter(year %in% input$year_choice_i6i7, species %in% input$species_i6i7i8) 
df_i7_filtered <- as(df_i6i7, "Spatial")

i7 <-  Atlas_i7_SpeciesMapRelativeCatches(df=df_i7_filtered, 
                              geomIdAttributeName="geom_id",
                              yearAttributeName="year", 
                              speciesAttributeName="species",                                         
                              valueAttributeName="value",
                          withSparql=FALSE
                          )

# i7

})

plotlyOutput("plot7")

Plot 6 Indicator I6 : Catches by 5x5 degrees

output$plot6 <- renderPlotly({ 


  if(wkt()!=new_wkt){

    df_i6i7 = st_read(con, 
                      query =  paste0("SELECT ogc_fid, geom_id, geom, year, species, country, value, count FROM public.i6i7i8 WHERE ST_Within(geom,ST_GeomFromText('",wkt(),"',4326)) AND species IN ('",paste0(input$species_i6i7i8,collapse="','"),"') AND year IN ('",paste0(input$year_choice_i6i7,collapse="','"),"');")
                      )
}else{
  df_i6i7=df_i6i7i8
}

# if(wkt()!=new_wkt){
#   df_i6i7i8 = st_read(con, 
#                       query =  paste0("SELECT ogc_fid, geom_id, geom, year, species, country, value, count FROM public.i6i7i8 WHERE ST_Within(geom,ST_GeomFromText('",wkt(),"',4326)) AND species IN ('",paste0(input$species_i6i7i8,collapse="','"),"') AND year IN ('",paste0(input$year_choice_i6i7,collapse="','"),"');")
#   )
# }else{
#   df_i6i7 <- df_i6i7i8
# }

# df_i6i7i8_filtered <- df_i6i7i8 %>% filter(year %in% input$year_choice_i6i7, species %in% input$species_i6i7i8) 
df_i6_filtered <- as(df_i6i7, "Spatial")

i6 <- Atlas_i6_SpeciesMap(df=df_i6_filtered,
                          geomIdAttributeName="geom_id",
                          yearAttributeName="year",
                          speciesAttributeName="species",
                          valueAttributeName="value",
                          withSparql=FALSE
                          )

})

plotlyOutput("plot6")