add functionality to create cubes via gbif - 1

source/functions/write_sql_query_occcubes.R

@@ -0,0 +1,66 @@
+write_sql_query_occcubes <- function(
+    species_keys = c(11,12,13),
+    year_begin,
+    year_end,
+    polygon
+){
+  paste0(
+    "
+SELECT
+\"year\",
+    GBIF_EEARGCode(
+      1000,
+      decimalLatitude,
+      decimalLongitude,
+      COALESCE(coordinateUncertaintyInMeters, 1000)
+    ) AS eeaCellCode,
+    classKey,
+    class,
+    speciesKey,
+    species,
+    COUNT(*) AS occurrences,
+    MIN(COALESCE(coordinateUncertaintyInMeters, 1000)) AS minCoordinateUncertaintyInMeters,
+    MIN(GBIF_TemporalUncertainty(eventDate)) AS minTemporalUncertainty,
+    IF(ISNULL(classKey), NULL, SUM(COUNT(*)) OVER (PARTITION BY classKey)) AS classCount
+  FROM
+    occurrence
+  WHERE
+    occurrenceStatus = 'PRESENT'
+    AND speciesKey IN (",
+    paste0(species_keys, collapse = ",")
+    ,
+    ")\nAND continent = 'EUROPE' ###
+    AND \"year\" >= ",year_begin,"
+    AND \"year\" <= ",year_end,"
+    AND hasCoordinate = TRUE
+    AND speciesKey IS NOT NULL
+    AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
+    AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
+    AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
+    AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
+AND (LOWER(identificationVerificationStatus) NOT IN (
+      'unverified',
+      'unvalidated',
+      'not validated',
+      'under validation',
+      'not able to validate',
+      'control could not be conclusive due to insufficient knowledge',
+      'uncertain',
+      'unconfirmed',
+      'unconfirmed - not reviewed',
+      'validation requested'
+      ) OR identificationVerificationStatus IS NULL)
+  GROUP BY
+    \"year\",
+    eeaCellCode,
+    classKey,
+    class,
+    speciesKey,
+    species
+  ORDER BY
+    \"year\" DESC,
+    eeaCellCode ASC,
+    speciesKey ASC;
+  ")
+  )
+}

source/gbif_occ_maps/1_download_cubes.R

@@ -0,0 +1,140 @@
+rm(list = ls())
+#
+# -----------------------------------------------------------------------------
+#
+# define polygon flanders + buffer
+buffer <- 1000*100 # in meters
+fla_borders <- sf::st_read("data/gis/prius/flanders_wgs84.geojson") # flanders
+fla_borders_buffer <- sf::st_buffer(x = fla_borders, dist = buffer)
+plot_check <- ggplot2::ggplot() + # plot to check
+  ggplot2::geom_sf(data = fla_borders_buffer, fill = "blue", size = 0.2) +
+  ggplot2::geom_sf(data = fla_borders, fill = "coral", size = 0.2)
+fla_borders_buffer_txt <- fla_borders_buffer |>
+  sf::st_geometry() |>
+  sf::st_as_text() |>
+  wk::wkt() |>
+  wk::wk_orient()
+# CHECK: https://docs.ropensci.org/rgbif/articles/getting_occurrence_data.html
+#
+# define gbif parameters
+scientific_names <- get(
+  load("data/processed/names_prius.Rda")
+) |>
+  purrr::pluck("data")  |>
+  dplyr::pull(dplyr::contains("scientific"))
+country <- "BE" # not used
+area_id <- "BEL.2_1" # flanders # not used
+# https://docs.ropensci.org/rgbif/articles/getting_occurrence_data.html
+basis_of_record <- c(
+  "OBSERVATION",
+  "HUMAN_OBSERVATION",
+  "MATERIAL_SAMPLE",
+  "LITERATURE",
+  "PRESERVED_SPECIMEN",
+  "UNKNOWN",
+  "MACHINE_OBSERVATION"
+) # so, everything but c("FOSSIL_SPECIMEN","LIVING_SPECIMEN")
+year_end <- lubridate::year(Sys.Date())
+year_begin <- year_end - 10
+hasCoordinate <- TRUE
+#
+# download
+gbif_download_args <- list(
+  rgbif::pred_in("scientificName", scientific_names),
+  #rgbif::pred("country", country),
+  #rgbif::pred("gadm", area_id),
+  rgbif::pred_within(fla_borders_buffer_txt),
+  rgbif::pred_in("basisOfRecord", basis_of_record),
+  rgbif::pred_gte("year", year_begin),
+  rgbif::pred_lte("year", year_end),
+  rgbif::pred("hasCoordinate", hasCoordinate)
+  #user = rstudioapi::askForPassword("GBIF username"),
+  #pwd = rstudioapi::askForPassword("GBIF password"),
+  #email = rstudioapi::askForPassword("Email address for notification")
+)
+#
+#
+#
+# set up sql query
+## see example for species list
+## https://raw.githubusercontent.com/damianooldoni/b3cubes-sql-examples/refs/heads/main/examples/other_examples/digital_cat_biodiversity_poland_strepsiptera.json
+sql_query <- c("
+SELECT
+\"year\",
+    GBIF_EEARGCode(
+      1000,
+      decimalLatitude,
+      decimalLongitude,
+      COALESCE(coordinateUncertaintyInMeters, 1000)
+    ) AS eeaCellCode,
+    classKey,
+    class,
+    speciesKey,
+    species,
+    COUNT(*) AS occurrences,
+    MIN(COALESCE(coordinateUncertaintyInMeters, 1000)) AS minCoordinateUncertaintyInMeters,
+    MIN(GBIF_TemporalUncertainty(eventDate)) AS minTemporalUncertainty,
+    IF(ISNULL(classKey), NULL, SUM(COUNT(*)) OVER (PARTITION BY classKey)) AS classCount
+  FROM
+    occurrence
+  WHERE
+    occurrenceStatus = 'PRESENT'
+    AND speciesKey IN (4480653, 4480642, 4480637, 4480628, 4480626, 4480624, 9719065)
+    AND continent = 'EUROPE'
+    AND \"year\" >= 1900
+    AND hasCoordinate = TRUE
+    AND speciesKey IS NOT NULL
+    AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
+    AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
+    AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
+    AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
+    AND LOWER(identificationVerificationStatus) NOT IN (
+      'unverified',
+      'unvalidated',
+      'not validated',
+      'under validation',
+      'not able to validate',
+      'control could not be conclusive due to insufficient knowledge',
+      'uncertain',
+      'unconfirmed',
+      'unconfirmed - not reviewed',
+      'validation requested'
+      )
+  GROUP BY
+    \"year\",
+    eeaCellCode,
+    classKey,
+    class,
+    speciesKey,
+    species
+  ORDER BY
+    \"year\" DESC,
+    eeaCellCode ASC,
+    speciesKey ASC;
+  ")
+
+
+
+
+
+gbif_download_key <- do.call(
+  eval(parse(text = "rgbif::occ_download")),
+  gbif_download_args
+)
+#
+# check status of download
+rgbif::occ_download_meta(key = gbif_download_key) |> purrr::pluck("status")
+#
+# save download key & metadata
+gbif_download_meta <- list(
+  key = gbif_download_key,
+  args = gbif_download_args,
+  date = Sys.Date()
+)
+save(gbif_download_meta,
+     file = paste0(
+       "data/raw/gbif_download_",
+       gbif_download_meta$key |> as.character(),
+       ".rda"
+     )
+)