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Create a presence-absence dataframe for a given occurrence record dataframe

Source: R/get_presence_absence.R
get_presence_absence.Rd

Use a dataframe output by SSARP::find_areas() to determine which species occur on specific islands by creating a presence-absence dataframe. A 1 represents presence and a 0 represents absence.

Usage

get_presence_absence(occs)

Arguments

occs

The dataframe output by SSARP::find_areas(), or if using a custom dataframe, ensure that it has the following named columns:

  • "areas" containing the areas associated with the land masses of interest

  • "Species" containing the names of the species living on those islands

  • A 6th column containing locality information. In the SSARP workflow, this column is called "First" and contains the country name

  • A 7th column containing locality information. In the SSARP workflow, this column is called "Second" and contains a province or island name

  • An 8th column containing locality information. In the SSARP workflow, this column is called "Third" and contains the island name if the 7th column does not contain the island name

Value

A dataframe with a row for each island in the given occurrence record dataframe and a column for each species. Within each species column, a 1 represents the presence of that species on the island corresponding to the given row, and a 0 represents the absence of that species on the island corresponding to the given row.

Examples

# The GBIF key for the Anolis genus is 8782549
#  Obtained with: key <- get_key(query = "Anolis", rank = "genus")
key <- 8782549
# Read in example dataset obtained through:
#  dat <- get_data(key = key, limit = 100)
dat <- read.csv(system.file("extdata",
                            "SSARP_Example_Dat.csv",
                            package = "SSARP"))
land <- find_land(occurrences = dat)
areas <- find_areas(occs = land)
#> ℹ Recording island names...
#> ℹ Assembling island dictionary...
#> ℹ Adding areas to final dataframe...
pres_abs <- get_presence_absence(areas)