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Visualise the biomes workflow (ranking, map and biome-class composition)

Source: R/biomes_visualise.R
biomes_visualise.Rd

Produces the publication figure of the biomes workflow for a set of occurrence records. Up to three panels are drawn and combined:

Usage

biomes_visualise(
  x,
  scheme = NULL,
  scheme_type = "all",
  biome = NULL,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  panels = c("rank", "map", "barplot"),
  legend_counts = TRUE,
  legend = TRUE,
  point_color = "#B20000",
  point_size = 0.25,
  combine = TRUE,
  verbose = FALSE
)

Arguments

x

A data frame with longitude/latitude columns, an sf spatial object, or a terra::SpatVector of point geometries.

scheme

Integer in 1:31 (biome scheme number). If NULL (default), the best-fitting scheme is chosen by biomes_rank() (within scheme_type).

scheme_type

Character. Methodological group to rank within when scheme is NULL; passed to biomes_rank(). Default "all".

biome

Optional single-layer terra::SpatRaster. If supplied it is mapped directly and only the map panel is available (no ranking).

lon, lat

Column names of longitude / latitude in x (data frame only). Defaults "decimalLongitude"/"decimalLatitude".

panels

Character vector, any subset of c("rank", "map", "barplot") (default all three). Panels are drawn and lettered in this order.

legend_counts

Logical. If TRUE (default), append the number of records per biome class to the map legend labels.

legend

Logical. If TRUE (default), draw the biome-class colour legend on the map panel.

point_color

Colour of the occurrence points. Default "#B20000".

point_size

Numeric size of the occurrence points. Default 0.25.

combine

Logical. When more than one panel is drawn: TRUE (default) combines them into one lettered figure (a, b, c); FALSE returns a named list of the individual panels (no letters). Ignored for a single panel (always returned as a bare ggplot).

verbose

Logical. Passed to biomes_rank(). Default FALSE.

Value

For a single panel, a ggplot object. For several panels: a combined cowplot object when combine = TRUE (default), or a named list of ggplot objects (rank, map, barplot) when combine = FALSE. Print to display or save with ggplot2::ggsave().

Details

  • rank: the data-driven ranking of the biome schemes (biomes_rank()): the composite score per scheme (best highlighted) next to the raw criterion values it averages (coverage, effective number of classes, granularity, ...).

  • map: the occurrence records (points) mapped over the chosen biome scheme, with the number of records per biome class optionally appended to the legend labels.

  • barplot: the number of occurrence records (left) and species (right) per biome class, with the biome-class names in the centre.

Which panels are drawn is controlled by panels; the panel letters (a, b, c) are assigned in drawing order, so selecting only rank and barplot labels them (a) and (b).

Examples

# \donttest{
data("biomes_example")
# full figure (rank + map + barplot), best scheme chosen automatically
biomes_visualise(biomes_example)
#> <SpatRaster> resampled to 5e+05 cells.


# only the map, for a fixed scheme
biomes_visualise(biomes_example, scheme = 1, panels = "map")
#> <SpatRaster> resampled to 5e+05 cells.


# map + barplot for the best vegetation scheme
biomes_visualise(biomes_example, scheme_type = "vegetation",
                 panels = c("map", "barplot"))
#> <SpatRaster> resampled to 5e+05 cells.

# }