Goal

The records were assigned to biomes in Step 3. This final step summarises the result per biome with biomes_tab() and visualises the whole workflow with biomes_visualise().

1. Tabulate records per biome

biomes_tab() counts occurrence records (one input row = one record) per biome and scheme, returning a long table with one row per (scheme, biome) pair:

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

The returned columns are scheme, biome and n. To count unique species per biome instead of records, deduplicate by species first:

library(dplyr)

classified |>
  distinct(species, Biome_Inventory_layer_01_name) |>
  biomes_tab()

2. Visualise the workflow

biomes_visualise() draws up to three panels for a set of occurrence records:

• rank: the ranking of the biome schemes (best highlighted);
• map: the occurrence records (red points) over the chosen scheme, with the number of records per biome appended to the legend labels;
• barplot: the number of records and species per biome.

By default all three are drawn and lettered a, b, c. If scheme is NULL, the best-fitting scheme is chosen by biomes_rank() (within definition).

biomes_visualise(bombacoideae_occurrences)               # rank + map + barplot

Select individual panels with panels; the panel letters adjust to the selection (e.g. panels = c("map", "barplot") labels them a and b):

# just the map, for a fixed scheme
biomes_visualise(bombacoideae_occurrences, scheme = 1, panels = "map")

The red points are the occurrence records you supplied. Drop the record counts from the legend labels with legend_counts = FALSE, or the whole colour legend with legend = FALSE. Save any panel with ggplot2::ggsave():

p <- biomes_visualise(bombacoideae_occurrences, scheme = 1, panels = "map", legend = FALSE)
ggplot2::ggsave("biome_map.jpg", p, width = 13, height = 8, dpi = 600)

The whole workflow in one call

Steps 1-4 are wrapped by biomes_full(), which by default ranks across all 31 schemes and uses the best one. No figure is drawn by default (plot = "none", the fastest option). plot = "all" returns the combined lettered figure in res$plot:

res <- biomes_full(x = bombacoideae_occurrences, plot = "all")   # scheme = "best"
res$scheme     # the chosen biome scheme number
res$table      # records per biome
res$plot       # the combined figure (rank + map + barplot)

A subset of c("rank", "map", "barplot") returns the panels individually (no panel letters), each in its own component res$rank, res$map, res$barplot:

res <- biomes_full(x = bombacoideae_occurrences, plot = c("rank", "map", "barplot"))
res$map        # just the map panel, on its own
res$barplot    # just the barplot panel

To force a specific scheme, pass its number (scheme = 1); to rank within one group, pass a biome definition (scheme = "vegetation"). Reach for the individual functions when you want to tweak a step; use biomes_full() when you want the standard pipeline in one call.

Done

That completes the four-step workflow: assemble → choose a scheme → classify → output and visualise. Back to Step 1.