plot.spgeoOUT: Plot Method for SpgeoOUT Objects

In azizka/speciesgeocodeR: Prepare Species Distributions for the Use in Phylogenetic Analyses

Plot Method for SpgeoOUT Objects

Description

The plotting method for objects of the class spgeoOUT. Depending on the type argument the function can be used to get an overview over the data or plot all elements of the object.

Usage

## S3 method for class 'spgeoOUT'
plot(x,  type = "summary", mode = "percent", ...)

Arguments

x	an object of the class spgeoOUT.
type	a character string. Controls which data shall be plotted. Default is to “summary”. See details for more information.
mode	a character string. Can be “percent” or “total” controls if percentage or total is shown for type = “species”. Default is “percent”.
...	additional arguments passed to other methods

Details

The output will be different depending on the type argument. type = “summary”: a map with all occurrence points and polygons (red points not classified to any polygon), the species number for all polygons, and if available, a heatplot visualizing the coexistence matrix; type = “species”: a bar chart for each input species showing the number of occurrences in each polygon; type = “polygons”: a bar chart for each input-polygon showing the number of occurrences for each species in the polygon; type = “speciesrichness”: a bar chart showing species number per polygon; type = “mapspecies”: one map per species showing all occurrence points in all polygons; type = “mappolygons”: a series of maps, showing each polygon and its close environment, with all samples classified to this polygon. Species are color-coded; type = “mapunclassified”: a map with all sample points that could not be classified to any polygon; type = “mapall”: a map of all occurrence points in the object.

See Also

summary.spgeoOUT

Examples

#simulate example occurrences
data(lemurs)
data(mdg_biomes)

outp <- SpGeoCod(lemurs, mdg_biomes, areanames = 'name')
## Not run: 
plot(outp)
plot(outp, type = "speciesrichness")
plot(outp, type = "mapall")

## End(Not run)

azizka/speciesgeocodeR documentation built on Sept. 5, 2023, 3:45 a.m.