Compute the mean of all unique pairwise great-circle distances between occurrence records for each species, using longitude/latitude coordinates (EPSG:4326). Distances are computed with sf::st_distance().
Arguments
- df
A data.frame (or tibble) containing species names and coordinates.
- species_col
Character. Column name containing species names. Default "species".
- lon_col
Character. Column name containing longitudes (decimal degrees). Default "lon".
- lat_col
Character. Column name containing latitudes (decimal degrees). Default "lat".
Value
A data.frame with columns:
species: unique species names
avg_distance_m: mean pairwise distance in meters
Details
For each species, the function:
Filters out rows with missing species or coordinates
Converts lon/lat to an sf point object with CRS = 4326
Builds a full distance matrix within the species
Extracts the upper triangle (unique pairs) and averages distances
Species with fewer than 2 valid records return NA.
Examples
# \donttest{
library(dplyr)
#>
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:terra’:
#>
#> intersect, union
#> The following objects are masked from ‘package:stats’:
#>
#> filter, lag
#> The following objects are masked from ‘package:base’:
#>
#> intersect, setdiff, setequal, union
library(sf)
#> Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE
# Create example occurrence data for 3 species
occurrences <- tibble(
species = c(
rep("Species_A", 4),
rep("Species_B", 5),
rep("Species_C", 2)
),
lon = c(
# Species A: widespread across Brazil
-43.2, -47.9, -38.5, -51.2,
# Species B: clustered in southeast
-43.9, -44.1, -43.7, -44.3, -43.8,
# Species C: only 2 points
-45.0, -46.0
),
lat = c(
# Species A
-22.9, -15.8, -12.9, -30.0,
# Species B
-19.9, -20.1, -19.8, -20.3, -20.0,
# Species C
-23.5, -24.0
)
)
# Calculate average pairwise distances
result <- occ.avg.dist(occurrences)
result
#> species avg_distance_m
#> 1 Species_A 1375543.80
#> 2 Species_B 41801.74
#> 3 Species_C 115972.99
# }