inst/shiny/modules/penvs_userBgExtent.R

In wallaceEcoMod/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.
# 
# penvs_userBgExtent.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/>.
# --------------------------------------------------------------------------
#
penvs_userBgExtent_module_ui <- function(id) {
  ns <- shiny::NS(id)
  tagList(
    span("Step 1:", class = "step"),
    span("Choose Background Extent", class = "stepText"), br(), br(),
    fileInput(ns("userBgShp"),
              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$div(title = paste0('Buffer area in degrees (1 degree = ~111 km). Exact',
                            ' length varies based on latitudinal position.'),
             numericInput(ns("userBgBuf"),
                          label = "Study region buffer distance (degree)",
                          value = 0, min = 0, step = 0.5)),
    tags$div(
      title = "Apply selection to ALL species loaded",
      checkboxInput(ns("batch1"), label = strong("Batch"), value = FALSE) # Check default (value = FALSE)
    ),
    actionButton(ns("goUserBg"), "Load"),
    tags$hr(class = "hrDotted"),
    span("Step 2:", class = "step"),
    span("Sample Background Points", class = "stepText"), br(), br(),
    strong(paste0('Mask predictor rasters by background extent and sample',
                  ' background points')), br(), br(),
    numericInput(ns("bgPtsNum"), label = "No. of background points",
                 value = 10000, min = 1, step = 1), # Check default (value = 10000)
    tags$div(
      title = "Apply selection to ALL species loaded",
      checkboxInput(ns("batch2"), label = strong("Batch"), value = FALSE) # Check default (value = FALSE)
    ),
    actionButton(ns("goBgMask"), "Sample"),
    tags$hr(class = "hrDashed"),
    actionButton(ns("goReset_penvs"), "Reset", class = 'butReset'),
    strong(" background")
  )
}

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

  logger <- common$logger
  spp <- common$spp
  allSp <- common$allSp
  curSp <- common$curSp
  envs.global <- common$envs.global
  envs <- common$envs
  bgExt <- common$bgExt
  occs <- common$occs

  observeEvent(input$goUserBg, {
    # ERRORS ####
    if (is.null(input$userBgShp)) {
      logger %>%
        writeLog(type = 'error',
                 'Background extent files not uploaded.')
      return()
    }


    # loop over all species if batch is on
    if (input$batch1 == TRUE) spLoop <- allSp() else spLoop <- curSp()

    # PROCESSING ####
    for (sp in spLoop) {
      # ERRORS ####
      if (is.null(spp[[sp]]$envs)) {
        logger %>% writeLog(
          type = 'error',
          hlSpp(sp),
          'Environmental variables missing. Obtain them in component 3.')
        return()
      }
      # FUNCTION CALL ####
      userBgExt <- penvs_userBgExtent(input$userBgShp$datapath,
                                      input$userBgShp$name,
                                      input$userBgBuf,
                                      spp[[sp]]$occs,
                                      logger,
                                      spN = sp)
      # LOAD INTO SPP ####
      spp[[sp]]$procEnvs$bgExt <- userBgExt

      # METADATA ####
      ##Record buffer size
      spp[[sp]]$rmm$code$wallace$bgBuf <- input$userBgBuf
      ##Record name of user provided background extent
      spp[[sp]]$rmm$data$occurrence$backgroundSampleSizeRule <- input$userBgShp$name
      # get extensions of all input files
      spp[[sp]]$rmm$rmm$code$wallace$userBgName  <-input$userBgShp$name
        paste0('User Polygon, ', input$bgBuf, ' degree buffer')
      exts <- sapply(strsplit(input$userBgShp$name, '\\.'),
                     FUN = function(x) x[2])
      if ('csv' %in% exts) {
        spp[[sp]]$rmm$code$wallace$userBgExt <- 'csv'
        spp[[sp]]$rmm$code$wallace$userBgPath <- input$userBgShp$datapath
      }
      else if ('shp' %in% exts) {
        spp[[sp]]$rmm$code$wallace$userBgExt <- 'shp'
        spp[[sp]]$rmm$code$wallace$userBgPath <- input$userBgShp$datapath
        # get index of .shp
        i <- which(exts == 'shp')
        shpName <- strsplit(input$userBgShp$name[i], '\\.')[[1]][1]
        spp[[sp]]$rmm$code$wallace$userBgShpParams <-
          list(dsn = input$userBgShp$datapath[i], layer = shpName)
      }
    }
  })

  observeEvent(input$goBgMask, {
    # WARNING ####
    if (input$bgPtsNum < 1) {
      logger %>% writeLog(type = 'warning',
                          "Enter a non-zero number of background points.")
      return()
    }
    req(bgExt())
    # loop over all species if batch is on
    if (input$batch2 == TRUE) spLoop <- allSp() else spLoop <- curSp()

    # PROCESSING ####
    for (sp in spLoop) {
      # FUNCTION CALL ####
      bgMask <- penvs_bgMask(spp[[sp]]$occs,
                             envs.global[[spp[[sp]]$envs]],
                             spp[[sp]]$procEnvs$bgExt,
                             logger,
                             spN = sp)
      req(bgMask)
      bgNonNA <- raster::ncell(bgMask) - raster::freq(bgMask, value = NA)[[1]]
      if ((bgNonNA + 1) < input$bgPtsNum) {
        logger %>%
          writeLog(
            type = "error", hlSpp(sp),
            "Number of requested background points (n = ", input$bgPtsNum, ") is ",
            "higher than the maximum points available on the background extent ",
            "(n = ", bgNonNA, "). Please reduce the number of requested points.")
        return()
      }
      bgPts <- penvs_bgSample(spp[[sp]]$occs,
                              bgMask,
                              input$bgPtsNum,
                              logger,
                              spN = sp)
      req(bgPts)
      withProgress(message = paste0("Extracting background values for ",
                                    spName(sp), "..."), {
                                      bgEnvsVals <- as.data.frame(raster::extract(bgMask, bgPts))
                                    })

      if (sum(rowSums(is.na(raster::extract(bgMask, spp[[sp]]$occs[ , c("longitude", "latitude")])))) > 0) {
        logger %>%
          writeLog(type = "error", hlSpp(sp),
                   "One or more occurrence points have NULL raster values.",
                   " This can sometimes happen for points on the margin of the study extent.",
                   " Please increase the buffer slightly to include them.")
        return()
      }

      # LOAD INTO SPP ####
      spp[[sp]]$procEnvs$bgMask <- bgMask
      # add columns for env variables beginning with "envs_" to bg tbl
      spp[[sp]]$bg <- cbind(scientific_name = paste0("bg_", sp), bgPts,
                            country = NA, state_province = NA, locality = NA,
                            year = NA, record_type = NA, catalog_number = NA,
                            institution_code = NA, elevation = NA,
                            uncertainty = NA, bgEnvsVals)
      # sample background points
      spp[[sp]]$bgPts <- bgPts

      # METADATA ####
      spp[[sp]]$rmm$data$occurrence$backgroundSampleSizeSet <- input$bgPtsNum
    }
  })

  # reset background button functionality
  observeEvent(input$goReset_penvs, {
    req(curSp())
    spp[[curSp()]]$procEnvs$bgExt <- NULL
    spp[[curSp()]]$procEnvs$bgMask <- NULL
    spp[[curSp()]]$bg <- NULL
    spp[[curSp()]]$bgPts <- NULL
    spp[[curSp()]]$rmm$data$occurrence$backgroundSampleSizeSet <- NULL
    logger %>% writeLog(
      hlSpp(curSp()), "Reset background extent and background points.")
  })

  return(list(
    save = function() {
      list(
        userBgBuf = input$userBgBuf,
        bgPtsNum = input$bgPtsNum
      )
    },
    load = function(state) {
      # Load
      updateNumericInput(session, "userBgBuf", value = state$userBgBuf)
      updateNumericInput(session, "bgPtsNum", value = state$bgPtsNum)
    }
  ))

  common$update_component(tab = "Map")
}

penvs_userBgExtent_module_map <- function(map, common) {
  spp <- common$spp
  curSp <- common$curSp
  occs <- common$occs

  if (is.null(spp[[curSp()]]$procEnvs$bgExt)) {
    map %>% clearAll() %>%
      addCircleMarkers(data = occs(), lat = ~latitude, lng = ~longitude,
                       radius = 5, color = 'red', fill = TRUE, fillColor = "red",
                       fillOpacity = 0.2, weight = 2, popup = ~pop)
  } else {
    map %>% clearAll() %>%
      addCircleMarkers(data = occs(), lat = ~latitude, lng = ~longitude,
                       radius = 5, color = 'red', fill = TRUE, fillColor = "red",
                       fillOpacity = 0.2, weight = 2, popup = ~pop)
    polys <- spp[[curSp()]]$procEnvs$bgExt@polygons[[1]]@Polygons
    if (length(polys) == 1) {
      xy <- list(polys[[1]]@coords)
    } else {
      xy <- lapply(polys, function(x) x@coords)
    }
    for (shp in xy) {
      map %>%
        addPolygons(lng = shp[, 1], lat = shp[, 2], weight = 4, color = "gray",
                    group = 'bgShp')
    }
    bb <- spp[[curSp()]]$procEnvs$bgExt@bbox
    map %>% fitBounds(bb[1], bb[2], bb[3], bb[4])
  }
}

penvs_userBgExtent_module_rmd <- function(species) {
  list(
  # Variables used in the module's Rmd code
    penvs_userBgExtent_knit = !is.null(species$rmm$code$wallace$userBgExt),
    bgShp_name_rmd = species$rmm$code$wallace$userBgShpParams[["layer"]],
    userBgBuf_rmd = species$rmm$code$wallace$bgBuf,
    bgPtsNum_rmd = species$rmm$data$occurrence$backgroundSampleSizeSet
  )
}