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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 class is a category within it; a biome scheme number (1-31) identifies a scheme. The
scheme_typeargument groups schemes by methodology.
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:
exp(H'),
the effective number of biome classes the records occupy (rewards
schemes that spread the data over several well-populated classes).The three criteria are min-max scaled to [0, 1] and
averaged (equal weights) into a composite score. The
best-scoring scheme is returned in
attr(ranking, "best_scheme").
ranking <- biomes_rank(biomes_example, 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.
Comparing schemes of different methodologies can mislead, so restrict
the ranking to one group with scheme_type:
r_veg <- biomes_rank(biomes_example, scheme_type = "vegetation", verbose = FALSE)
attr(r_veg, "best_scheme")
table(biomes_information$scheme_type) # how many schemes per groupscheme_type = "all" (the default) ranks all 31 schemes.
Other groups are "climate", "vegetation",
"land_cover", "ecoregion",
"integrative" and "anthropogenic".
The rank panel of biomes_visualise() shows
the composite score per scheme with the best scheme highlighted:
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.
You have a chosen biome scheme. Continue with Step 3: Occurrences-to-biome classification.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.