Map species occurrences — occmap • rSDM

Plot map of species occurrences (or any set of point coordinates) on top of different background layers.

occmap(
  locs,
  ras = NULL,
  bg = "Esri.WorldImagery",
  type = c("base", "ggplot", "leaflet"),
  pcol = "red",
  alpha = 1,
  psize = 1,
  add = FALSE,
  prev.map = NULL,
  ...
)

Arguments

locs: An sf::sf() or terra::SpatVector() object with point coordinates, e.g. as generated from locs2sf() or locs2vect().
ras: A terra::SpatRaster() object to be used as background for points. If NULL (default), a background map defined by bg will be used.
bg: Character. Type of background map to be used if ras is not provided. bg should be one of the providers listed in maptiles::get_tiles() if type is 'base' or 'ggplot', or one of the providers listed in leaflet::addProviderTiles() if type is 'leaflet'.
type: Character. One of "base", "ggplot" or "leaflet" to define the type of map produced.
pcol: Colour to be used for points. Default is "red".
alpha: Colour transparency for points, between 0 (fully transparent) and 1 (fully opaque).
psize: Point size. Default is 1 (cex = 1).
add: Logical. Add locs coordinates to a previous 'base' map? (e.g. for a new species).
prev.map: Map to be used as basemap to add further points (only applicable for "leaflet" and "ggplot" map types).
...: additional parameters to be passed to terra::plot() if type = "base" tidyterra::geom_spatraster() if type = "ggplot" or leaflet::addCircleMarkers() if type = "leaflet".

Value

A map plus a leaflet or ggplot object, depending on type.

Examples

if (FALSE) { # interactive()
## Example coordinates
locs <- data.frame(lon = c(-5.8, -5.5, -5.9), lat = c(35.7, 36.2, 36.5))
locs <- locs2sf(locs, crs = 4326)

## Default map
occmap(locs, psize = 6)
occmap(locs, psize = 6, bg = "CartoDB.Positron") # Change background

## Interactive (leaflet) map
occmap(locs, psize = 6, type = "leaflet")
occmap(locs, psize = 6, type = "leaflet", bg = "CartoDB.Positron")

## ggplot map
occmap(locs, psize = 6, type = "ggplot")

## Adding points to a previous map
new.locs <- data.frame(lon = c(-5.8, -5.4), lat = c(36.2, 36.5))
new.locs.sf <- locs2sf(new.locs, crs = 4326)

## base
map <- occmap(locs, psize = 6)
occmap(new.locs.sf, add = TRUE, psize = 6, pcol = "blue")

## Adding points to a previous map (leaflet)
map <- occmap(locs, psize = 6, type = "leaflet")
occmap(new.locs.sf, prev.map = map, psize = 6, pcol = "blue")

## Adding points to a previous map (ggplot)
map <- occmap(locs, psize = 6, type = "ggplot")
occmap(new.locs.sf, prev.map = map, psize = 6, pcol = "blue")
}