inst/shiny/modules/occs_paleoDb.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.
# 
# occs_paleoDb.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/>.
# --------------------------------------------------------------------------
#
# occs_paleoDb_module_ui <- function(id) {
#   ns <- shiny::NS(id)
#   tagList(
#     shinyWidgets::pickerInput(
#       ns("timeInterval"),
#       label = "Select interval",
#       choices = setNames(as.list(c('Quaternary', 'Holocene', 'Pleistocene',
#                                    'Late Pleistocene', 'Middle Pleistocene',
#                                    'Calabrian', 'Gelasian')),
#                          c('Quaternary [0 - 2.588]',
#                            '-- Holocene [0 - 0.0117]',
#                            '-- Pleistocene [0.0117 - 2.588]',
#                            '---- Late Pleistocene [0.0117 - 0.126]',
#                            '---- Middle Pleistocene [0.126 - 0.781]',
#                            '---- Calabrian [0.781 - 1.806]',
#                            '---- Gelasian [1.806 - 2.588]')),
#       multiple = FALSE),
#     tags$div(title = 'Examples: Canis lupus, Crocuta crocuta',
#              textInput(ns("spNamePB"), label = "Enter species scientific name",
#                        placeholder = 'format: Genus species')),
#     tags$div(title = paste0('Maximum number of occurrences recovered from',
#                             ' databases. Downloaded records are not sorted',
#                             ' randomly: rows are always consistent between',
#                             ' downloads.'),
#              numericInput(ns("occsNumPB"), "Set maximum number of occurrences",
#                           value = 0, min = 0, max = 500)),
#     actionButton(ns("goPaleoDbOccs"), "Query Database")
#   )
# }
#
# occs_paleoDb_module_server <- function(input, output, session, common) {
#   logger <- common$logger
#   spp <- common$spp
#
#   observeEvent(input$goPaleoDbOccs, {
#     # WARNING ####
#     if (input$occsNumPB < 1) {
#       logger %>% writeLog(type = 'warning', "Enter a non-zero number of ocurrences.")
#       return()
#     }
#
#     # FUNCTION CALL ####
#     occsTbls <- occs_paleoDb(input$spNamePB, input$occsNumPB, input$timeInterval,
#                              logger)
#
#     req(occsTbls)
#
#     # LOAD INTO SPP ####
#     occsOrig <- occsTbls$orig
#     occs <- occsTbls$cleaned
#     sp <- fmtSpN(input$spNamePB)
#     sp <- paste0(toupper(substring(sp, 1, 1)), substring(sp, 2, nchar(sp)))
#     # if species name is already in list, overwrite it
#     if (!is.null(spp[[sp]])) spp[[sp]] <- NULL
#     # add two copies of occs dataset -- "occs" will be altered during session,
#     # while "occsOrig" will be preserved in this state
#     # rmm is the range model metadata object
#     spp[[sp]] <- list(occs = occs,
#                       occData = list(occsOrig = occsOrig,
#                                      occsCleaned = occs),
#                       rmm = rangeModelMetadata::rmmTemplate(),
#                       rmd = list())
#
#     # REFERENCES ####
#     knitcitations::citep(citation("paleobioDB"))
#
#     # METADATA ####
#     spp[[sp]]$rmm$data$occurrence$taxon <- sp
#     spp[[sp]]$rmm$data$occurrence$dataType <- "presence only"
#     spp[[sp]]$rmm$data$occurrence$presenceSampleSize <- nrow(occs)
#     spp[[sp]]$rmm$data$occurrence$yearMin <- paste(min(occs$late_age), "mya")
#     spp[[sp]]$rmm$data$occurrence$yearMax <- paste(max(occs$early_age), "mya")
#     spp[[sp]]$rmm$code$wallace$occsNum <- input$occsNumPB
#     spp[[sp]]$rmm$code$wallace$occsRemoved <- nrow(occsOrig) - nrow(occs)
#     spp[[sp]]$rmm$data$occurrence$sources <- "paleobioDb"
#     spp[[sp]]$rmm$code$wallace$timeInterval <- input$timeInterval
#
#     common$update_component(tab = "Map")
#   })
#
#   return(list(
#     save = function() {
#       list(
#         spNamePB = input$spNamePB,
#         occsNumPB = input$occsNumPB,
#         timeInterval = input$timeInterval
#       )
#     },
#     load = function(state) {
#       updateTextInput(session, "spNamePB", value = state$spNamePB)
#       updateNumericInput(session, "occsNumPB", value = state$occsNumPB)
#       shinyWidgets::updatePickerInput(session, "timeInterval",
#                                       selected = input$timeInterval)
#     }
#   ))
#
# }
#
# occs_paleoDb_module_map <- function(map, common) {
#   spp <- common$spp
#   curSp <- common$curSp
#   occs <- spp[[curSp()]]$occData$occsCleaned
#   map %>% clearAll() %>%
#     addCircleMarkers(data = occs, lat = ~latitude, lng = ~longitude,
#                      radius = 5, color = 'red', fill = TRUE, fillColor = "red",
#                      fillOpacity = 0.2, weight = 2, popup = ~pop) %>%
#     zoom2Occs(occs)
# }
#
# occs_paleoDb_module_rmd <- function(species) {
#   # Variables used in the module's Rmd code
#   list(
#     occs_paleoDb_knit = species$rmm$data$occurrence$sources == "paleobioDb",
#     occsNumPB_rmd = species$rmm$code$wallace$occsNum,
#     timeInterval_rmd = species$rmm$code$wallace$timeInterval
#   )
# }
#