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Plot a raster showing the richness of taxa

Source: R/pbdb_geographic_functions.R
pbdb_map_richness.Rd

Creates a SpatRaster object and a plot with richness of species, genera, families, etc. per cell.

Usage

pbdb_map_richness(
  data,
  rank = c("species", "genus", "family", "order", "class", "phylum"),
  do_plot = TRUE,
  res = 5,
  col_int = "white",
  col_ocean = "black",
  col_rich = c("light blue", "blue"),
  title = "Taxonomic richness",
  ...
)

Arguments

data

Input data frame. This data frame is the output of the pbdb_occurrences() function using the argument show = c("coords", "classext"). See also Details and Examples.

rank

Taxon rank for which richness is calculated. The options are: "species", "genus", "family", "order", "class" or "phylum". The default value is "species".

do_plot

Logical. If TRUE, the function produces a plot in addition to returning a SpatRaster.

res

The resolution of the SpatRaster object (in decimal degrees). See terra::res().

col_int

The colour of the mainland.

col_ocean

The colour of the ocean.

col_rich

Two or more colours that are used to generate the colour gradient showing the richness per cell in the map.

title

A title for the plot, to be positioned to the right of the legend.

...

Other parameters. See par() and map().

Value

A SpatRaster object with the richness of the specified taxon rank per cell. This SpatRaster object has the resolution that was specified in the res argument. The default is res = 5. Users that wish to work with objects of this type should load package terra.

Details

The argument show = c("coords", "classext") in the pbdb_occurrences() function is required. We recommend the use of a cairo device (X11()) for better visualization of the graphs. See Examples.

See also

See pbdb_occurrences(), map(), par() and colors() help pages.

Examples

if (FALSE) {
  data <- pbdb_occurrences(
    limit = 1000, vocab = "pbdb", base_name = "mammalia",
    show = c("classext", "coords")
  )
  X11(width = 13, height = 7.8)
  pbdb_map_richness(data, res = 8, rank = "genus")
  pbdb_map_richness(data, res = 8, rank = "family")
  ## Get the raster object without plotting the map
  pbdb_map_richness(data, res = 8, rank = "family", do_plot = FALSE)
}