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Build a presence-absence database from multi-species occurrence data

Source: R/get_absences.R
get_absences.Rd

Converts a database containing occurrence records for multiple species into a presence-absence database, either for every species present in the data or for a specified subset of target species. For each target species, its own records are coded as presences and the records of all other species are recoded as absences for that species.

Usage

get_absences(
  data,
  x = "x",
  y = "y",
  species = "species",
  target_species = NULL,
  pr_ab_name = "pr_ab"
)

Arguments

data

data.frame or tibble. A table with occurrence records for one or more species, including columns for species identity and x/y coordinates.

x

character. Name of the column in data with the x (longitude) coordinate. Default "x".

y

character. Name of the column in data with the y (latitude) coordinate. Default "y".

species

character. Name of the column in data with the species name/identifier. Default "species".

target_species

character vector. One or more species names to build presence-absence data for. If NULL (default), a presence-absence database is built for every unique species found in data[[species]].

pr_ab_name

character. Name to give the presence-absence column in the output, coded 1 for presences and 0 for absences. Default "pr_ab".

Value

A tibble with columns species, x, y (using the names supplied in the species, x, and y arguments) and the presence-absence column named according to pr_ab_name. For each species in target_species (or each unique species in data, if target_species = NULL), the output contains one presence-absence block: records belonging to that species are coded 1, and records of all other species are recoded as belonging to that species with a value of 0. Blocks for all target species are stacked row-wise, so the returned tibble has nrow(data) * length(sp) rows, where sp is the set of target species.

Details

Only the species, x, and y columns are retained in the output; any other columns present in data (e.g., environmental covariates or metadata) are dropped. If you need those columns downstream, re-join them after calling this function.

Because absences for a given target species are drawn from every other species' occurrence records, duplicate x/y coordinates across species in the input will produce duplicate absence coordinates in the output.

Examples

if (FALSE) { # \dontrun{
data <- data.frame(
  species = c("sp1", "sp1", "sp2", "sp2", "sp3"),
  x = c(-74.1, -74.2, -73.9, -73.8, -74.0),
  y = c(4.6, 4.65, 4.7, 4.72, 4.68)
)

# Presence-absence database for every species in the data
get_absences(data, x = "x", y = "y", species = "species", target_species = NULL, pr_ab_name = "pr_ab")

# Presence-absence database for a single target species
get_absences(data, x = "x", y = "y", species = "species", target_species = "sp1", pr_ab_name = "pr_ab")

# Presence-absence database for a subset of species, with a custom
# presence-absence column name
get_absences(data, x = "x", y = "y", species = "species", target_species = c("sp1", "sp2"), pr_ab_name = "occ")
} # }