Bug Hunter

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
# Data wrangling
# library(stringr)
library(dplyr)
library(fs)
library(ruODK)

# Visualisation
library(skimr)
library(knitr)
library(DT)

# Dissemination
library(readr)
# library(ckanr)
# library(googledrive)

# Spatial: see also vignette "spatial"
library(leaflet)
# library(rgeos)
# library(sf)

# Set ruODK defaults to an ODK Central form's OData Service URL
ruODK::ru_setup(
  svc=paste0("https://odkc.dbca.wa.gov.au/v1/projects/5/forms/build_Bug-Hunter_1607931390.svc"),
  tz = "Australia/Perth", # your local timezone
  odkc_version = 1.0,     # your ODKC version, only needed if <=0.7
  verbose = FALSE)

loc <- fs::path("media")
fs::dir_create(loc)

Download data

ft <- ruODK::odata_service_get()
# ft %>% knitr::kable(.)

data <- ruODK::odata_submission_get(
  table = ft$url[1],
  local_dir = loc, 
  wkt = TRUE
)

Analyse and visualise data

# skimr::skim(data)
# dplyr::glimpse(data)
# DT::datatable(head(data))
data %>% 
  dplyr::group_by(reporter, encounter_subject) %>% 
  dplyr::tally() %>% 
  dplyr::arrange(reporter, -n) %>% 
  reactable::reactable(sortable = TRUE, filterable = TRUE, searchable = TRUE)

leaflet::leaflet(height = 600) %>%
  leaflet::addProviderTiles("Esri.WorldImagery", group = "Basemap") %>%
  leaflet::addProviderTiles("OpenStreetMap.Mapnik", group = "Basemap",
    options = leaflet::providerTileOptions(opacity = 0.35)) %>%
  leaflet.extras::addFullscreenControl(pseudoFullscreen = TRUE) %>% 
  leaflet::clearBounds() %>%
  leaflet::addAwesomeMarkers(
    data = data,
    # 
    # # Adjust to your coordinate field names
    # 
    lng = ~encounter_location_longitude, 
    lat = ~encounter_location_latitude, 
    icon = leaflet::makeAwesomeIcon(
      text = ~ stringr::str_sub(data$encounter_subject, 1,1)
    ),
    # 
    # # With your own field names
    # 
    label = ~ glue::glue("{start_time}"),
    popup = ~ glue::glue(
      "<h3>{encounter_subject}</h3>",
      "Seen on {start_time} by {reporter}</br>",
      '<div><a href="{encounter_photo}" target="_" rel="nofollow">',
      '<img src="{encounter_photo}" height="150px"',
      'alt="{encounter_subject} - Click to enlarge"></img></a></div>'
    ),
    group = "Bugs"
    # 
    # # If there are many submissions, cluster markers for performance:
    # clusterOptions = leaflet::markerClusterOptions()
  ) %>%
  leaflet::addLayersControl(
    baseGroups = c("Basemap"),
    overlayGroups = c("Bugs"),
    options = leaflet::layersControlOptions(collapsed = FALSE)
  )

Export

#------------------------------------------------------------------------------#
# Prepare report and products as local files
#
rep_fn <- "my_report.html" # The file name you save this template under
data_fn <- here::here(loc, "data.csv") %>% as.character()           # Main data
data_sub1_fn <- here::here(loc, "data_sub1.csv") %>% as.character() # Sub table 1
data_sub2_fn <- here::here(loc, "data_sub2.csv") %>% as.character() # Sub table 2
zip_fn <- "products.zip" # Attachments as one zip file (top level)

# Write data tbls to CSV files
readr::write_csv(data, path = data_fn)
readr::write_csv(data_sub1, path = data_sub1_fn)
readr::write_csv(data_sub2, path = data_sub2_fn)

# Compress everything into `zip_fn`, retain relative path to `loc`
zip(zipfile = zip_fn, files = fs::dir_ls(loc))

#------------------------------------------------------------------------------#
# CKAN
#
# Upload to a CKAN data catalogue (needs url and API key of a write permitted user)
# See ROpenSci package ckanr
ckanr::ckanr_setup(url = Sys.getenv("CKAN_URL"), key = Sys.getenv("CKAN_KEY"))
ckan_ds_name <- "my-ckan-dataset-slug"

# Run once to create resources on an existing dataset, then comment out
d <- ckanr::package_show(ckan_ds_name)
res_data_main <- ckanr::resource_create(
  package_id = d$id, name="Main data", upload = data_fn)
res_data_sub1 <- ckanr::resource_create(
  package_id = d$id, name="Nested data table 1", upload = data_sub1_fn)
res_data_sub2 <- ckanr::resource_create(
  package_id = d$id, name="Nested data table 2", upload = data_sub2_fn)
# add remaining tables
if (fs::file_exists(rep_fn)){
res_report <- ckanr::resource_create(
  package_id = d$id, name="Data report", upload = rep_fn)
}

if (fs::file_exists(zip_fn)){
res_zip <- ckanr::resource_create(
  package_id = d$id, name="All data and attachments", upload = zip_fn)
}
# Paste res_data_main$id over RID and keep here, repeat for each resource
r <- ckanr::resource_update(res_data_main$id, path = data_fn)
r <- ckanr::resource_update(res_data_sub1$id, path = data_sub1_fn)
r <- ckanr::resource_update(res_data_sub2$id, path = data_sub2_fn)
if (fs::file_exists(rep_fn)){
  r <- ckanr::resource_update(res_report$id, path = rep_fn)
}
r <- ckanr::resource_update(res_zip$id, path = zip_fn)

#------------------------------------------------------------------------------#
# Google Drive
#
# Run once per machine, then comment out:
googledrive::drive_auth(use_oob = TRUE)

# Upload to Google Drive
gd_fn <- "My Google Drive folder name"
googledrive::drive_ls(gd_fn) %>% googledrive::drive_rm(.)  # Wipe older outputs
if (fs::file_exists(rep_fn)){
  googledrive::drive_upload(rep_fn, path=rep_fn)             # Report as HTML
}
googledrive::drive_upload(data_fn, path=data_fn)           # Main data as CSV
googledrive::drive_upload(data_sub1_fn, path=data_sub1_fn) # Sub table 1 as CSV
googledrive::drive_upload(data_sub2_fn, path=data_sub2_fn) # Sub table 2 as CSV
googledrive::drive_upload(zip_fn, path=zip_fn)             # All outputs as ZIP