Step 2: Choice of a biome scheme

Goal

Step 1 gave us occurrence records and the 31 biome schemes. With 31 schemes to choose from, this step picks the one that best fits your data, so the choice is explicit and reproducible rather than defaulting to a familiar scheme.

Terms. A biome scheme is one of the 31 classification systems; a biome is a category within it; a biome scheme number (1-31) identifies a scheme. A biome definition is the concept on which a scheme delimits its biomes; the definition argument restricts the ranking to the schemes sharing one definition.

1. Rank the schemes for your data

biomes_rank() scores every scheme for your occurrences and proposes a single best-fitting scheme. Each scheme is rated on three complementary, data-driven criteria:

The three criteria are min-max scaled to [0, 1] across the compared schemes and averaged (equal weights) into a composite score. The best-scoring scheme is returned in attr(ranking, "best_scheme").

Because the scaling is relative to the compared schemes, a composite score is only comparable among schemes that were ranked together, and a scaled value of 0 means “lowest among the compared schemes”, not zero. A criterion that does not vary among the compared schemes is left out of the composite (see attr(ranking, "criteria_used")), and a single compared scheme gets no composite score. Ties in the composite score are broken by the publication year of the scheme (more recent first; see tiebreaker).

ranking <- biomes_rank(bombacoideae_occurrences, verbose = FALSE)
best    <- attr(ranking, "best_scheme")
best
head(ranking)

The result is a data frame with one row per scheme; the key columns are scheme (the biome scheme number), scheme_name, composite_score and is_best.

Rank within one biome definition

Comparing schemes built on different biome definitions can mislead, so restrict the ranking to the schemes sharing one definition with definition:

r_veg <- biomes_rank(bombacoideae_occurrences, definition = "vegetation", verbose = FALSE)
attr(r_veg, "best_scheme")

table(biomes_information$biome_definition)   # how many schemes per group

definition = "all" (the default) ranks all 31 schemes. The biome definitions are "climate", "vegetation", "land_cover", "ecoregion", "integrative" and "anthropogenic".

2. Inspect the ranking

The rank panel of biomes_visualise() shows the composite score per scheme with the best scheme highlighted:

biomes_visualise(bombacoideae_occurrences, panels = "rank")

Treat the ranking as a shortlist, not an authoritative answer: the most suitable scheme ultimately depends on your research question. Inspect the criterion-specific columns of the ranking and use biomes_info() to pick the scheme whose concept and resolution match your data.

The integer in attr(ranking, "best_scheme") is exactly the biome scheme number you pass as scheme to the classification and visualisation functions next.