occmap: Map species occurrences

In Pakillo/rSDM: Species distribution and niche modelling in R

Map species occurrences

Description

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

Usage

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

## 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")

Pakillo/rSDM documentation built on March 1, 2025, 12:30 a.m.