BeeBDC (version 1.2.0)

countryOutlieRs: Flag country-level outliers with a provided checklist.

Description

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

Usage

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

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.

See Also

continentOutlieRs() for implementation at the continent level. Implementation at the continent level may be lighter and more manageable on the data side of things where country-level checklists don't exist. Additionally, see beesChecklist() for input data. Note, not all columns are necessary if you are building your own dataset. At a minimum you will need validName, country, iso_a3_eh (to match rnaturalearth).

Examples

if(requireNamespace("rnaturalearthdata")){
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)
table(beesRaw_out$.countryOutlier, useNA = "always")
} # END if require