Step 3: Occurrences-to-biome classification

Goal

With a biome scheme chosen in Step 2, biomes_classify() assigns one biome per occurrence record. You select the scheme by its biome scheme number (1-31), the same number biomes_rank() returns as the best scheme.

Terms. Classifying here means assigning each occurrence record to a biome (e.g. savanna) of the chosen biome scheme (identified by its biome scheme number).

1. Classify occurrence records into biomes

biomes_classify() takes a table of points (or an sf / SpatVector) and returns the input data with the biome assignment appended on the right. Pick the scheme with the scheme argument; you never handle SpatRaster objects yourself.

classified <- biomes_classify(bombacoideae_occurrences, scheme = 1)
head(classified)

A new column Biome_Inventory_layer_01_name has been added (the column names carry the raster layer names of the packaged stack). The appended columns use the suffixes _value (raster code) and _name (biome name). Records that fall outside every biome of a scheme (e.g. coastal records or small islands missing from a coarse map) are, by default, labelled "no_biome" rather than dropped, so the counts stay complete:

table(classified$Biome_Inventory_layer_01_name, useNA = "ifany")

Handling off-map records explicitly and identically across schemes matters, because the amount and spatial pattern of unassigned records differs between schemes, and is itself one of the ranking criteria in Step 2.

2. Common variations

# Several schemes at once, one column per scheme
biomes_classify(bombacoideae_occurrences, scheme = c(1, 25)) |> head(3)

# Keep both the raster value and the biome name
biomes_classify(bombacoideae_occurrences, scheme = 1, value = "both") |> head(3)

# Return only the classification columns (drop the input)
biomes_classify(bombacoideae_occurrences, scheme = 1, append = FALSE) |> head(3)

# Keep NA for off-map points instead of the "no_biome" label
class_na <- biomes_classify(bombacoideae_occurrences, scheme = 1, na = NA)
sum(is.na(class_na$Biome_Inventory_layer_01_name))

For a scheme outside the packaged stack, pass your own single-layer terra::SpatRaster via biome = instead of a scheme number.