paleobioDB (version 0.7.0)

pbdb_map_richness: pbdb_map_richness

Description

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

Usage

pbdb_map_richness (data, rank="species", do.plot=TRUE, res=5,
col.int="white", col.ocean="black",
col.rich=c("light blue","blue"),...)

Arguments

data

Input dataframe. This dataframe is the output of pbdb_occurrences function using the argument: show = c("phylo", "coords", "ident"). See too: Details and Examples

rank

To set which taxon rank you are interested for calculate richness. The options are: "species", "genus", "family", "order", "class" or "phylum")

do.plot

Logical; TRUE the function returns a RasterLayer and a plot.

res

The resolution of the RasterLayer object (in decimal degrees). See: raster

col.int

The colour of the mainland

col.ocean

The colour of the ocean

col.rich

Two or more colours. To generate the colour gradient used to show the richness per cell in map

...

Others parameters. See par and map

Value

A RasterLayer object and a plot with richness of species, genera, families, etc. per cell. This RasterLayer object have the resolution controlled by the argument res. The default is res=1.

Details

CAUTION! The argument show = "coords" in 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

# NOT RUN {
data<- pbdb_occurrences (limit=1000, vocab= "pbdb", base_name="mammalia",
show=c("phylo","coords","ident"))
X11(width=13, height=7.8)
pbdb_map_richness (data,res=8,rank="genus")
pbdb_map_richness (data,res=8,rank="family")
## to obtain the raster file and not plot the map
pbdb_map_richness (data,res=8,rank="family",do.plot=F)
# }
# NOT RUN {
# }