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(pacman)
library(sf)
library(sp)
library(ggplot2)
library(plyr)
library(plotly)

#######################
##Database Identifiers:
source(file = "~/Desktop/CODES/IRDTunaAtlas/credentials.R")
source("https://raw.githubusercontent.com/juldebar/IRDTunaAtlas/master/R/TunaAtlas_i4_SpeciesMonthByOcean.R")

Column {data-width=350}

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

wkt <- reactiveVal('POLYGON((-180 -90, 180 -90, 180 90, -180 90, -180 -90))') 
new_wkt <- 'POLYGON((-180 -90, 180 -90, 180 90, -180 90, -180 -90))'


query_i4 <- "select species, year, month, ocean, value from public.i4 ;"
df_i4 <- st_read(con, query=query_i4)
species = unique(df_i4$species)
year = unique(df_i4$year)

# selectInput widget

selectInput("species_choice", label = h3("Select species for i4 "), choices = species, selected = c("SKJ","YFT","BET"),multiple = TRUE)
selectInput("year_choice", label = h3("Select year for i4"), choices = year, selected = c("2000","2001","2002"),multiple = TRUE)


# textOutput(wkt())

renderPrint({ 
  paste0("Your current selection for i4: ", input$species_choice," and ",input$year_choice)
  query_i4 <- paste0("SELECT species, ocean, year, month, sum(value) as value, unit, st_collect(geom) FROM public.i4_spatial WHERE ST_Within(geom,ST_GeomFromText('",wkt(),"',4326)) GROUP BY species, ocean, year, month,unit;")
})

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,])))
            new_wkt <- 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,new_wkt)
            textOutput("wkt")
        })

Column {data-width=650}

Plot 4 Indicator I4 : Catches by month and by ocean

# renderPlotly({
renderPlot({

# https://mrjoh3.github.io/2018/12/26/shiny-image-gallery-examples/
# https://mrjoh3.github.io/p/shiny-image-gallery-examples/


if(wkt()!=new_wkt){
  df_i4 = st_read(con, query =  paste0("SELECT species, ocean, year, month, sum(value) as value, unit, st_collect(geom) FROM public.i4_spatial WHERE ST_Within(geom,ST_GeomFromText('",wkt(),"',4326)) GROUP BY species, ocean, year, month, unit ;"))
}
  #Filtering input dataset with selected parameters

df_i4_filtered <- df_i4 %>% filter(year %in% input$year_choice, species %in% input$species_choice) 
# df_i4_filtered <- df_i4 %>% filter(year %in% input$year_choice, ocean %in% input$ocean_choice, species %in% input$species_choice) 

i4 <- Atlas_i4_SpeciesMonthByOcean(df=as.data.frame(df_i4_filtered), 
                                          oceanAttributeName="ocean", 
                                          yearAttributeName="year", 
                                          monthAttributeName="month",
                                          speciesAttributeName="species", 
                                          valueAttributeName="value",
                                   withSparql=FALSE
                                      )
i4    
})

# plotlyOutput("plot4")