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Countries of occurrence and biogeographical realm(s) from a range

Source: R/countries.R
countries_of_occurrence.Rd

Derives the list of countries a taxon occurs in - and an approximate biogeographical realm - by intersecting its range with the public Natural Earth country base map, mirroring the "countries of occurrence" and "realms" supporting information that the IUCN Red List requires/recommends and that sRedList extracts automatically (Cazalis et al. 2024).

Usage

countries_of_occurrence(
  range,
  points = NULL,
  scale = c("medium", "small", "large")
)

Arguments

range

An sf/sfc polygon delimiting the range (e.g. the EOO hull from calc_eoo), or an sf of occurrence points. Any CRS is accepted (it is transformed to WGS84 internally).

points

Optional sf of occurrence POINT geometries used to set the Extant / Possibly Extant presence flag. NULL (default) means the presence is taken from range itself when it is a set of points, otherwise every overlapping country is Possibly Extant.

scale

Natural Earth scale passed to rnaturalearth::ne_countries ("small", "medium" (default) or "large").

Value

A data.frame with one row per country: country, presence ("Extant"/"Possibly Extant"), n_records (occurrences in that country), continent and realm. Rows are ordered by presence then country. An empty data.frame (with a message) is returned when rnaturalearth is not installed or no country overlaps.

Details

Following the Red List convention, every country the range polygon overlaps is reported, and each is flagged by presence:

  • Extant - the country holds at least one occurrence record;

  • Possibly Extant - the country overlaps the range but holds no record in the supplied points.

When no polygon is supplied (fewer than three points, so no EOO hull) the countries are taken from the points alone and are all reported as Extant.

Realm. The biogeographical realm is a coarse approximation derived from the continent of each country (Neotropical, Nearctic, Afrotropical, Palearctic, Indomalayan, Australasian, Oceanian or Antarctic); it is exact for the South-American ranges mappingAS is built around but should be checked for taxa spanning continental transitions (e.g. North/Central America, North Africa, South-East Asia), where realm boundaries do not follow country borders.

References

Cazalis V. et al. (2024) Accelerating and standardising IUCN Red List assessments with sRedList. Biological Conservation 298:110761. doi:10.1016/j.biocon.2024.110761

See also

calc_eoo, assess_species

Examples

# \donttest{
f <- system.file("extdata", "example_occurrences.csv", package = "mappingAS")
occ <- read_occurrences(f)
sp1 <- occ[occ$species == occ$species[1], ]
# Needs the 'rnaturalearth' package (Suggests):
countries_of_occurrence(calc_eoo(sp1)$hull, points = sp1)
#>   country presence n_records     continent       realm
#> 1  Brazil   Extant         5 South America Neotropical
# }