Flag country-level outliers with a provided checklist.

This function flags country-level outliers using the checklist provided with this package. For additional context and column names, see beesChecklist().

countryOutlieRs(
  checklist = NULL,
  data = NULL,
  keepAdjacentCountry = TRUE,
  pointBuffer = NULL,
  scale = 50,
  stepSize = 1e+06,
  mc.cores = 1
)

Arguments

checklist: A data frame or tibble. The formatted checklist which was built based on the Discover Life website.
data: A data frame or tibble. The a Darwin Core occurrence dataset.
keepAdjacentCountry: Logical. If TRUE, occurrences in countries that are adjacent to checklist countries will be kept. If FALSE, they will be flagged.
pointBuffer: Numeric. A buffer around points to help them align with a country or coastline. This provides a good way to retain points that occur right along the coast or borders of the maps in rnaturalearth
scale: Numeric. The value fed into the map scale parameter for rnaturalearth::ne_countries()'s scale parameter: Scale of map to return, one of 110, 50, 10 or 'small', 'medium', 'large', where smaller numbers are higher resolution. WARNING: This function is tested on 110 and 50.
stepSize: Numeric. The number of occurrences to process in each chunk. Default = 1000000.
mc.cores: Numeric. If > 1, the function will run in parallel using mclapply using the number of cores specified. If = 1 then it will be run using a serial loop. NOTE: Windows machines must use a value of 1 (see ?parallel::mclapply). Additionally, be aware that each thread can use large chunks of memory. If the cores throw issues, consider setting mc.cores to 1. Default = 1.

Value

The input data with two new columns, .countryOutlier or .sea. There are three possible values for the new column: TRUE == passed, FALSE == failed (not in country or in the ocean), NA == did not overlap with rnaturalearth map.

Examples

library(magrittr)
  # Load in the test dataset
beesRaw <- BeeBDC::beesRaw
  # For the sake of this example, use the testChecklist
system.file("extdata", "testChecklist.rda", package="BeeBDC") |> load()
  # For real examples, you might download the beesChecklist from FigShare using 
  #  [BeeBDC::beesChecklist()]

beesRaw_out <- countryOutlieRs(checklist = testChecklist,
                               data = beesRaw %>%
                               dplyr::filter(dplyr::row_number() %in% 1:50),
                               keepAdjacentCountry = TRUE,
                               pointBuffer = 1,
                               scale = 50,
                               stepSize = 1000000,
                               mc.cores = 1)
#> Spherical geometry (s2) switched off
#>  - Extracting country data from points...
#>  - Buffering failed points by pointBuffer...
#>  - Prepare the neighbouring country dataset...
#> although coordinates are longitude/latitude, st_intersects assumes that they
#> are planar
#>  - Compare points with the checklist...
#>  - Combining data...
#>  - Sorting and removing potentially duplicated buffered points...
#>  - Finished. 
#> We have matched 25 records to their exact country and 2 to an adjacent country
#> We failed to match 0 occurrences to any 'exact' or 'neighbouring' country.
#> There are 23 'NA' occurrences for the .countryOutlier column.
#> 
#> countryOutlieRs:
#> Flagged 0  for country outlier and flagged  0  for in the .sea records.
#> Three columns were added to the database:
#>  1.  The '.countryOutlier' column was added which is a filtering column. 
#>  2.  The 'countryMatch' columns indicates exact, neighbour, or noMatch. 
#>  3. The '.sea' column was added as a filtering column for points in the ocean.  The '.sea' column includes the user input buffer in its calculation.
#>  - Completed in 1.55 secs
table(beesRaw_out$.countryOutlier, useNA = "always")
#> 
#> TRUE <NA> 
#>   27   23