Pushing new code for the web app

check_ebird_checklists/check_ebird_checklists_fcn.R

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+# Check eBird Checklist
+# Author: Linus Blomqvist
+# Adaptation of code from Raphaël Nussbaumer
+# See https://github.com/Zoziologie/Check-eBird-Checklist
+
+# Load packages
+library(tidyverse)
+library(auk)
+library(DT)
+library(ggplot2)
+library(writexl)
+library(glue)
+
+# Create function
+create_chk <- function(txt_file) {
+
+  obs_0 <- read_ebd(txt_file)
+
+  obs_0 <- obs_0 %>%
+    filter(all_species_reported == TRUE)
+
+  obs <- obs_0 %>%
+    mutate(
+      group_id = checklist_id,
+      checklist_id = sampling_event_identifier
+    ) %>%
+    select(c(
+      "group_id", "checklist_id", "taxonomic_order", "common_name", "observation_count",
+      "locality", "observation_date", "time_observations_started", "observer_id",
+      "protocol_type", "duration_minutes", "effort_distance_km", "number_observers",
+      "all_species_reported", "has_media"))
+
+  c <- obs %>%
+    mutate(
+      observation_count_num = as.numeric(ifelse(observation_count == "X", NA, observation_count))
+    ) %>% 
+    group_by(group_id) %>%
+    mutate(
+      number_species = n(),
+      number_distinct_count = n_distinct(observation_count),
+      median_count = median(observation_count_num, na.rm = T),
+      number_media = sum(has_media)
+    ) %>%
+    ungroup() %>%
+    select(-c(group_id, taxonomic_order, common_name, observation_count, observation_count_num, has_media)) %>%
+    unique()
+
+  c <- c %>%
+    mutate(
+      observation_date = ymd(observation_date),
+      time_observations_started = hms(time_observations_started, quiet = T),
+      checklist_link = paste0("<a href='https://ebird.org/checklist/", str_extract(checklist_id, "^[^,]+"), "' target='_blank'>", checklist_id, "</a>"),
+      all_species_reported = all_species_reported & protocol_type != "Incidental"
+    )
+
+  chk <- c %>% 
+    mutate(
+      chk_ampm = (time_observations_started > hm("22:00") | time_observations_started < hm("4:00")) & 
+        (time_observations_started + minutes(duration_minutes) < hm("6:00")) & 
+        number_species > 10,
+      chk_midnight = time_observations_started == hms("00:00:00"),
+      chk_high_number_species = number_species>70,
+      chk_only_one_species = all_species_reported & number_species==1 & duration_minutes > 5,
+      chk_same_count_all_species = all_species_reported & median_count>0 & number_distinct_count==1 & number_species>2,
+      chk_too_long_distance = effort_distance_km > 20,
+      chk_multi_day = time_observations_started + minutes(duration_minutes) > hours(24),
+      chk_too_many_observers = number_observers > 30,
+      chk_too_short_duration = all_species_reported & number_species/duration_minutes > 10,
+      chk_too_fast = effort_distance_km/duration_minutes*60 > 60,
+      chk_complete_media = all_species_reported & number_media==number_species,
+      chk_not_stationary = protocol_type == "Stationary" & number_species>50,
+      chk_specialized_protocol = !(protocol_type %in% c("Historical", "Traveling", "Incidental", "Stationary")),
+      chk_not_traveling = protocol_type=="Traveling" & effort_distance_km < 0.03
+    ) %>% 
+    mutate(across(starts_with("chk_"), ~replace_na(., FALSE)))
+
+  chk <- chk %>%
+    mutate(dubious = ifelse(rowSums(.[,16:29]) >= 1, TRUE, FALSE)) %>%
+    filter(dubious == TRUE)
+
+  chk <- chk %>%
+    select(-c(time_observations_started, all_species_reported, number_distinct_count,
+           median_count, number_media, checklist_link, dubious))
+
+  return(chk)
+}

check_ebird_checklists/run_shiny_app.R

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+# Set working directory
+setwd("/Users/linusblomqvist/Library/CloudStorage/Dropbox/Birding/ebird_R/Check-eBird-Checklist/check_ebird_checklists")
+
+# Run app locally
+library(shiny)
+source("server.R")
+source("ui.R")
+shinyApp(ui, server)
+
+# Deploy to shinyapps.io
+library(rsconnect)
+deployApp()

check_ebird_checklists/server.R

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+# Source function
+source("check_ebird_checklists_fcn.R")
+
+options(shiny.maxRequestSize=100*1024^2)
+
+server <- function(input, output) {
+
+  datasetInput <- reactive({
+    req(input$upload)
+    # input$file1 will be NULL initially. After the user selects
+    # and uploads a file, it will be a data frame with 'name',
+    # 'size', 'type', and 'datapath' columns. The 'datapath'
+    # column will contain the local filenames where the data can
+    # be found.
+    inFile <- input$upload
+
+    if (is.null(inFile))
+      return(NULL)
+
+    create_chk(inFile$datapath)
+  })
+
+  output$contents <- renderDataTable({
+    datasetInput()
+  })
+
+  output$downloadData <- downloadHandler(
+    filename = "check_ebird_checklist.csv",
+    content = function(file) {
+      write.csv(datasetInput(), file, row.names = FALSE)
+    }
+  )
+}

check_ebird_checklists/ui.R

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+ui <- fluidPage(
+  titlePanel("Check eBird Checklists"),
+  sidebarLayout(
+    sidebarPanel(
+      fileInput("upload", "Choose .txt file",
+                buttonLabel = "Upload...", multiple = TRUE, accept = ".txt"),
+      hr(),
+      downloadButton(
+        "downloadData",
+        label = "Download spreadsheet",
+        class = NULL,
+        icon = shiny::icon("download")
+      )
+    ),
+    mainPanel(p("This web app implements code from Raphaël Nussbaumer (https://github.com/Zoziologie/Check-eBird-Checklist) to detect eBird checklists with potential errors."),
+              p("First upload a .txt file containing eBird data, downloaded from https://ebird.org/data/download. Once that's uploaded, click the download link and it will give you a .csv file with a list of problematic checklists.")
+  )
+)
+)

check_ebird_checklists_run.R

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+# Check ebird checklists run script
+# Author: Linus Blomqvist
+
+# Source function
+source("check_ebird_checklists_fcn.R")
+
+# Specify text file (put path and file name within quotation marks)
+# This is the file you would download from https://ebird.org/data/download
+# When downloading this file you can specify area, date range, etc
+txt_file <- ""
+
+# Run function
+chk <- create_chk(txt_file)
+
+# Export as xlsx (change name manually within quotation marks)
+write_xlsx(chk, "")