Count Presences of Species within a Specified Area — count

This function counts the number of occurrences of specified species within a defined area. The area can be specified using a shapefile or a two-letter country code. The function uses the rgbif package to query species occurrences and returns a data.frame with the results.

Usage

count_presences(species, shapefile = NULL, country = NULL)

Arguments

species: A data.frame containing the columns family, genus, and species. These should be the taxonomic details of the species for which you want to count occurrences.
shapefile: A shapefile (with lat/long coordinates) defining the area of interest. The function will create a minimum bounding rectangle around the shapefile to query the species occurrences. Default is NULL.
country: A two-letter country code (e.g., "DK" for Denmark) to define the area of interest. Default is NULL.

Value

A data.frame with columns family, genus, species, and N where N represents the number of occurrences of each species within the defined area.

Examples

# Example species data.frame
species <- structure(list(family = "Polytrichaceae", genus = "Atrichum",
                          species = "Atrichum undulatum"), row.names = c(NA, -1L),
                     class = c("tbl_df", "tbl", "data.frame"))

# Example 1: Using a country code
df_country <- count_presences(species, country = "DK")
print(df_country)
#>            family    genus            species     N
#>            <char>   <char>             <char> <num>
#> 1: Polytrichaceae Atrichum Atrichum undulatum  1596

# Example 2: Using a shapefile
# Assuming "Aarhus.shp" is in the working directory
f <- system.file("ex/Aarhus.shp", package="SpeciesPoolR")
df_shapefile <- count_presences(species, shapefile = f)
print(df_shapefile)
#>            family    genus            species     N
#>            <char>   <char>             <char> <num>
#> 1: Polytrichaceae Atrichum Atrichum undulatum    76