inst/shiny/modules/xfer_area.R

In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

# Wallace EcoMod: a flexible platform for reproducible modeling of
# species niches and distributions.
#
# xfer_area.R
# File author: Wallace EcoMod Dev Team. 2023.
# --------------------------------------------------------------------------
# This file is part of the Wallace EcoMod application
# (hereafter “Wallace”).
#
# Wallace is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License,
# or (at your option) any later version.
#
# Wallace is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
# --------------------------------------------------------------------------
#
xfer_area_module_ui <- function(id) {
  ns <- shiny::NS(id)
  tagList(
    span("Step 1:", class = "step"),
    span("Choose Study Region", class = "stepText"), br(), br(),
    selectInput(ns('xferExt'), label = "Select method",
      choices = list("Draw polygon" = 'xfDraw',
                     "User-specified polygon" = 'xfUser')),
    conditionalPanel(sprintf("input['%s'] == 'xfUser'", ns("xferExt")),
      fileInput(ns("userXfShp"),
                label = paste0('Upload polygon in shapefile (.shp, .shx, .dbf) or ',
                               'CSV file with field order (longitude, latitude)'),
                accept = c(".csv", ".dbf", ".shx", ".shp"), multiple = TRUE),
      tags$div(title = paste0('Buffer area in degrees (1 degree = ~111 km). Exact',
                              ' length varies based on latitudinal position.'),
        numericInput(ns("userXfBuf"), label = "Study region buffer distance (degree)",
                     value = 0, min = 0, step = 0.5))),
    conditionalPanel(sprintf("input['%s'] == 'xfDraw'", ns("xferExt")),
      p("Draw a polygon and select buffer distance"),
      tags$div(title = paste0('Buffer area in degrees (1 degree = ~111 km). Exact',
                              ' length varies based on latitudinal position.'),
        numericInput(ns("drawXfBuf"), label = "Study region buffer distance (degree)",
                     value = 0, min = 0, step = 0.5))),
    actionButton(ns("goxferExtArea"), "Create"), br(),
    tags$hr(class = "hrDotted"),
    span("Step 2:", class = "step"),
    span("Transfer", class = "stepText"), br(),
    p("Transfer model to transfer extent (red) "),
    tags$div(
      title = paste0(
        'Create binary map of predicted presence/absence assuming ',
        'all values above threshold value represent presence. Also ',
        'can be interpreted as a "potential distribution" (see ',
        'guidance).'),
      selectInput(ns('threshold'), label = "Set threshold",
                  choices = list("No threshold" = 'none',
                                 "Minimum Training Presence" = 'mtp',
                                 "10 Percentile Training Presence" = 'p10',
                                 "Quantile of Training Presences" = 'qtp'))),
    conditionalPanel(sprintf("input['%s'] == 'qtp'", ns("threshold")),
      sliderInput(ns("trainPresQuantile"), "Set quantile",
                  min = 0, max = 1, value = .05)),
    conditionalPanel(paste0("input['", ns("threshold"), "'] == 'none'"),
                     uiOutput(ns("noThrs"))),
    actionButton(ns('goTransferArea'), "Transfer"),
    tags$hr(class = "hrDashed"),
    actionButton(ns("goResetXfer"), "Reset", class = 'butReset'),
    strong(" transfer extent ")
  )
}

xfer_area_module_server <- function(input, output, session, common) {

  spp <- common$spp
  evalOut <- common$evalOut
  envs <- common$envs
  envs.global <- common$envs.global
  rmm <- common$rmm
  curSp <- common$curSp
  curModel <- common$curModel
  logger <- common$logger

  output$noThrs <- renderUI({
    ns <- session$ns
    req(curSp(), evalOut())
    if (spp[[curSp()]]$rmm$model$algorithms != "BIOCLIM") {
      h5("Prediction output is the same as Visualize component ")
    }
  })

  observeEvent(input$goxferExtArea, {
    # ERRORS ####
    if (is.null(spp[[curSp()]]$visualization$mapPred)) {
      logger %>% writeLog(type = 'error',
          'Calculate a model prediction in model component before transfering.')
      return()
    }
    if (input$xferExt == 'xfDraw') {
      if (is.null(spp[[curSp()]]$polyXfXY)) {
        logger %>% writeLog(type = 'error',
            paste0("The polygon has not been drawn and finished. Please use the ",
                   "draw toolbar on the left-hand of the map to complete the ",
                   "polygon."))
        return()
      }
    }
    if (input$xferExt == 'xfUser') {
      if (is.null(input$userXfShp$datapath)) {
        logger %>% writeLog(type = 'error', "Specified filepath(s) ")
        return()
      }
    }


    # FUNCTION CALL ####
    if (input$xferExt == 'xfDraw') {
      polyXf <- xfer_draw(spp[[curSp()]]$polyXfXY, spp[[curSp()]]$polyXfID,
                          input$drawXfBuf, logger, spN = curSp())
      if (input$drawXfBuf == 0 ) {
        logger %>% writeLog(
          hlSpp(curSp()), 'Draw polygon without buffer.')
      } else {
        logger %>% writeLog(
          hlSpp(curSp()), 'Draw polygon with buffer of ', input$drawXfBuf,
          ' degrees.')
      }
      # METADATA ####
      polyX <- printVecAsis(round(spp[[curSp()]]$polyXfXY[, 1], digits = 4))
      polyY <- printVecAsis(round(spp[[curSp()]]$polyXfXY[, 2], digits = 4))
      spp[[curSp()]]$rmm$code$wallace$drawExtPolyXfCoords <-
        paste0('X: ', polyX, ', Y: ', polyY)
      spp[[curSp()]]$rmm$code$wallace$XfBuff <- input$drawXfBuf
    }

    if (input$xferExt == 'xfUser') {
      polyXf <- xfer_userExtent(input$userXfShp$datapath, input$userXfShp$name,
                                input$userXfBuf, logger, spN = curSp())
      # ERRORS ####
      # Check that the extents of raster and transfer extent intersects
      polyXf_sfc <- sf::st_as_sfc(polyXf) #convert poly to sfc
      envs_ext <- methods::as(raster::extent(envs()),'SpatialPolygons')
      envs_sfc <- sf::st_as_sfc(envs_ext) #convert envs to sfc
      #set crs to match
      if (sf::st_crs(polyXf_sfc) != sf::st_crs(envs_sfc)) {
        sf::st_crs(polyXf_sfc) <- sf::st_crs(envs_sfc)
        logger %>%
          writeLog(type = 'error', 'CRS was automatically set to match environmental variables.')
        return()
      }
      if (!sf::st_intersects(polyXf_sfc, envs_sfc, sparse = FALSE)[1,1]) {
        logger %>%
          writeLog(type = 'error', 'Extents do not overlap.')
        return()
      }

      # METADATA ####
      spp[[curSp()]]$rmm$code$wallace$XfBuff <- input$userXfBuf
      # get extensions of all input files
      exts <- sapply(strsplit(input$userXfShp$name, '\\.'),
                     FUN = function(x) x[2])
      if('csv' %in% exts) {
        spp[[curSp()]]$rmm$code$wallace$userXfExt <- 'csv'
        spp[[curSp()]]$rmm$code$wallace$userXfPath <- input$userXfShp$datapath
      }
      else if('shp' %in% exts) {
        spp[[curSp()]]$rmm$code$wallace$userXfExt <- 'shp'
        # get index of .shp
        i <- which(exts == 'shp')
        shpName <- strsplit(input$userXfShp$name[i], '\\.')[[1]][1]
        spp[[curSp()]]$rmm$code$wallace$userXfShpParams <-
          list(dsn = input$userXfShp$datapath[i], layer = shpName)
      }
    }

    # LOAD INTO SPP ####
    spp[[curSp()]]$transfer$xfExt <- polyXf

    common$update_component(tab = "Map")
  })

  observeEvent(input$goTransferArea, {
    # ERRORS ####
    if (is.null(spp[[curSp()]]$visualization$mapPred)) {
      logger %>%
        writeLog(type = 'error',
                 'Calculate a model prediction in model component before transfering.')
      return()
    }
    if (is.null(spp[[curSp()]]$transfer$xfExt)) {
      logger %>% writeLog(type = 'error', 'Select transfer extent first.')
      return()
    }
    # Check that the extents of raster and transfer extent intersects
      Xfer_sfc <- sf::st_as_sfc(spp[[curSp()]]$transfer$xfExt) #convert xfrExt to sfc
      envs_ext <- methods::as(raster::extent(envs()),'SpatialPolygons')
      envs_sfc <- sf::st_as_sfc(envs_ext) #convert envs to sfc
    if (!sf::st_intersects(Xfer_sfc, envs_sfc, sparse = FALSE)[1,1]) {
      logger %>%
        writeLog(type = 'error', 'Extents do not overlap.')
      return()
    }

    if (is.null(envs())) {
      logger %>%
        writeLog(
          type = 'error',
          'Environmental variables missing. Obtain them in component 3.')
      return()
    } else {
      diskRast <- raster::fromDisk(envs.global[[spp[[curSp()]]$envs]])
      if (diskRast) {
        if (class(envs.global[[spp[[curSp()]]$envs]]) == "RasterStack") {
          diskExist <- !file.exists(envs.global[[spp[[curSp()]]$envs]]@layers[[1]]@file@name)
        } else if (class(envs.global[[spp[[curSp()]]$envs]]) == "RasterBrick") {
          diskExist <- !file.exists(envs.global[[spp[[curSp()]]$envs]]@file@name)
        }
        if (diskExist) {
          logger %>%
            writeLog(
              type = 'error',
              'Environmental variables missing. Please upload again.')
          return()
        }
      }
    }

    # FUNCTION CALL ####
    predType <- rmm()$prediction$notes
    if (spp[[curSp()]]$rmm$model$algorithms == "BIOCLIM") {
      xferArea.out <- xfer_area(evalOut = evalOut(),
                                curModel = curModel(),
                                envs = envs(),
                                xfExt = spp[[curSp()]]$transfer$xfExt,
                                alg = spp[[curSp()]]$rmm$model$algorithms,
                                logger,
                                spN = curSp())
    } else {
      xferArea.out <- xfer_area(evalOut = evalOut(),
                                curModel = curModel(),
                                envs = envs(),
                                xfExt = spp[[curSp()]]$transfer$xfExt,
                                alg = spp[[curSp()]]$rmm$model$algorithms,
                                outputType = predType,
                                clamp = rmm()$model$algorithm$maxent$clamping,
                                logger,
                                spN = curSp())
    }

    xferExt <- xferArea.out$xferExt
    xferArea <- xferArea.out$xferArea

    # PROCESSING ####
    # generate binary prediction based on selected thresholding rule
    # (same for all Maxent prediction types because they scale the same)
    occPredVals <- spp[[curSp()]]$visualization$occPredVals

    if(!(input$threshold == 'none')) {
      if (input$threshold == 'mtp') {
        thr <- stats::quantile(occPredVals, probs = 0)
      } else if (input$threshold == 'p10') {
        thr <- stats::quantile(occPredVals, probs = 0.1)
      } else if (input$threshold == 'qtp'){
        thr <- stats::quantile(occPredVals, probs = input$trainPresQuantile)
      }
      xferAreaThr <- xferArea > thr
      logger %>% writeLog(hlSpp(curSp()), "Transfer of model to new area with threshold ",
                          input$threshold, ' (', formatC(thr, format = "e", 2), ').')
    } else {
      xferAreaThr <- xferArea
      logger %>% writeLog(hlSpp(curSp()), "Transfer of model to new area with ",
                          predType, ' output.')
    }
    raster::crs(xferAreaThr) <- raster::crs(envs())
    # rename
    names(xferAreaThr) <- paste0(curModel(), '_thresh_', predType)

    # LOAD INTO SPP ####
    spp[[curSp()]]$transfer$xfEnvs <- xferExt
    spp[[curSp()]]$transfer$mapXfer <- xferAreaThr
    spp[[curSp()]]$transfer$mapXferVals <- getRasterVals(xferAreaThr, predType)

    # METADATA ####
    spp[[curSp()]]$rmm$code$wallace$transfer_curModel <- curModel()
    spp[[curSp()]]$rmm$code$wallace$transfer_area <- TRUE
    spp[[curSp()]]$rmm$data$transfer$environment1$minVal <-
      printVecAsis(raster::cellStats(xferExt, min), asChar = TRUE)
    spp[[curSp()]]$rmm$data$transfer$environment1$maxVal <-
      printVecAsis(raster::cellStats(xferExt, max), asChar = TRUE)
    if (spp[[curSp()]]$rmm$data$environment$sources == 'WorldClim 2.1') {
      spp[[curSp()]]$rmm$data$transfer$environment1$yearMin <- 1970
      spp[[curSp()]]$rmm$data$transfer$environment1$yearMax <- 2000
    }
    spp[[curSp()]]$rmm$data$transfer$environment1$resolution <-
      paste(round(raster::res(xferExt)[1] * 60, digits = 2), "degrees")
    spp[[curSp()]]$rmm$data$transfer$environment1$extentSet <-
      printVecAsis(as.vector(xferExt@extent), asChar = TRUE)
    spp[[curSp()]]$rmm$data$transfer$environment1$extentRule <-
      "transfer to user-selected new area"
    spp[[curSp()]]$rmm$data$transfer$environment1$sources <-
      spp[[curSp()]]$rmm$data$environment$sources
    spp[[curSp()]]$rmm$prediction$transfer$environment1$units <-
      ifelse(predType == "raw", "relative occurrence rate", predType)
    spp[[curSp()]]$rmm$prediction$transfer$environment1$minVal <-
      printVecAsis(raster::cellStats(xferAreaThr, min), asChar = TRUE)
    spp[[curSp()]]$rmm$prediction$transfer$environment1$maxVal <-
      printVecAsis(raster::cellStats(xferAreaThr, max), asChar = TRUE)
    if(!(input$threshold == 'none')) {
      spp[[curSp()]]$rmm$prediction$transfer$environment1$thresholdSet <- thr
      if (input$threshold == 'qtp') {
        spp[[curSp()]]$rmm$code$wallace$transferQuantile <- input$trainPresQuantile
      } else {
        spp[[curSp()]]$rmm$code$wallace$transferQuantile <- 0
      }
    } else {
      spp[[curSp()]]$rmm$prediction$transfer$environment1$thresholdSet <- NULL
    }
    spp[[curSp()]]$rmm$prediction$transfer$environment1$thresholdRule <- input$threshold

    if (!is.null(spp[[curSp()]]$rmm$model$algorithm$maxent$clamping)) {
      spp[[curSp()]]$rmm$prediction$transfer$environment1$extrapolation <-
        spp[[curSp()]]$rmm$model$algorithm$maxent$clamping
    }
    spp[[curSp()]]$rmm$prediction$transfer$notes <- NULL

    common$update_component(tab = "Map")
  })

  # Reset Transfer Extent button functionality
  observeEvent(input$goResetXfer, {
    spp[[curSp()]]$polyXfXY <- NULL
    spp[[curSp()]]$polyXfID <- NULL
    spp[[curSp()]]$transfer <- NULL
    logger %>% writeLog("Reset transfer extent.")
  })

  return(list(
    save = function() {
      list(
        xferExt = input$xferExt,
        userXfBuf = input$userXfBuf,
        drawXfBuf = input$drawXfBuf,
        threshold = input$threshold,
        trainPresQuantile = input$trainPresQuantile
      )
    },
    load = function(state) {
      updateSelectInput(session, 'xferExt', selected = state$xferExt)
      updateNumericInput(session, 'userXfBuf', value = state$userXfBuf)
      updateNumericInput(session, 'drawXfBuf', value = state$drawXfBuf)
      updateSelectInput(session, 'threshold', selected = state$threshold)
      updateSliderInput(session, 'trainPresQuantile', value = state$trainPresQuantile)
    }
  ))
}

xfer_area_module_map <- function(map, common) {

  spp <- common$spp
  evalOut <- common$evalOut
  curSp <- common$curSp
  rmm <- common$rmm
  mapXfer <- common$mapXfer

  # Map logic
  map %>% leaflet.extras::addDrawToolbar(
    targetGroup = 'draw', polylineOptions = FALSE, rectangleOptions = FALSE,
    circleOptions = FALSE, markerOptions = FALSE, circleMarkerOptions = FALSE,
    editOptions = leaflet.extras::editToolbarOptions()
  )
  # Add just transfer Polygon
  req(spp[[curSp()]]$transfer$xfExt)
  polyXfXY <- spp[[curSp()]]$transfer$xfExt@polygons[[1]]@Polygons
  if(length(polyXfXY) == 1) {
    shp <- list(polyXfXY[[1]]@coords)
  } else {
    shp <- lapply(polyXfXY, function(x) x@coords)
  }
  bb <- spp[[curSp()]]$transfer$xfExt@bbox
  bbZoom <- polyZoom(bb[1, 1], bb[2, 1], bb[1, 2], bb[2, 2], fraction = 0.05)
  map %>% clearAll() %>% removeImage('xferRas') %>%
    fitBounds(bbZoom[1], bbZoom[2], bbZoom[3], bbZoom[4])
  for (poly in shp) {
    map %>% addPolygons(lng = poly[, 1], lat = poly[, 2], weight = 4,
                        color = "red",group = 'bgShp')
  }
  req(evalOut(), spp[[curSp()]]$transfer$xfEnvs)
  mapXferVals <- spp[[curSp()]]$transfer$mapXferVals
  rasCols <- c("#2c7bb6", "#abd9e9", "#ffffbf", "#fdae61", "#d7191c")
  # if threshold specified
  if(rmm()$prediction$transfer$environment1$thresholdRule != 'none') {
    rasPal <- c('gray', 'red')
    map %>% removeControl("xfer") %>%
      addLegend("bottomright", colors = c('gray', 'red'),
                title = "Thresholded Suitability<br>(Transferred)",
                labels = c("predicted absence", "predicted presence"),
                opacity = 1, layerId = 'xfer')
  } else {
    # if no threshold specified
    legendPal <- colorNumeric(rev(rasCols), mapXferVals, na.color = 'transparent')
    rasPal <- colorNumeric(rasCols, mapXferVals, na.color = 'transparent')
    map %>% removeControl("xfer") %>%
      addLegend("bottomright", pal = legendPal,
                title = "Predicted Suitability<br>(Transferred)",
                values = mapXferVals, layerId = 'xfer',
                labFormat = reverseLabel(2, reverse_order = TRUE))
  }
  # map model prediction raster and transfer polygon
  map %>% clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>%
    addRasterImage(mapXfer(), colors = rasPal, opacity = 0.7,
                   layerId = 'xferRas', group = 'xfer', method = "ngb")
  for (poly in shp) {
    map %>% addPolygons(lng = poly[, 1], lat = poly[, 2], weight = 4,
                        color = "red", group = 'xfer', fill = FALSE)
  }
}

xfer_area_module_rmd <- function(species) {
  # Variables used in the module's Rmd code
  list(
    xfer_area_knit = !is.null(species$rmm$code$wallace$transfer_area),
    curModel_rmd = species$rmm$code$wallace$transfer_curModel,
    outputType_rmd = species$rmm$prediction$notes,
    alg_rmd = species$rmm$model$algorithms,
    clamp_rmd = species$rmm$model$algorithm$maxent$clamping,
    ###arguments for creating extent
    polyXfXY_rmd = if(!is.null(species$rmm$code$wallace$drawExtPolyXfCoords)){
    printVecAsis(species$polyXfXY)} else {NULL},
    polyXfID_rmd =  if(!is.null(species$rmm$code$wallace$drawExtPolyXfCoords)){
     species$polyXfID} else {0},
    BgBuf_rmd = species$rmm$code$wallace$XfBuff,
    ##Determine the type of transfer extent to use correct RMD function
    xfer_area_extent_knit = !is.null(species$rmm$code$wallace$userXfShpParams),
    ##Use of threshold for transfer
    xfer_area_threshold_knit = !is.null(species$rmm$prediction$transfer$environment1$thresholdSet),
    xfer_thresholdRule_rmd = species$rmm$prediction$transfer$environment1$thresholdRule,
    xfer_threshold_rmd = if (!is.null(species$rmm$prediction$transfer$environment1$thresholdSet)){
    species$rmm$prediction$transfer$environment1$thresholdSet} else {0},
    xfer_probQuantile_rmd = species$rmm$code$wallace$transferQuantile

  )
}