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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(rSDM)

Let's create example point coordinates and convert them to a spatial (sf) object:

locs <- data.frame(lon = c(-5.8, -5.5, -5.9), lat = c(35.7, 36.2, 36.5))
locs <- locs2sf(locs, crs = 4326)
locs

Note that SpatVector objects (from terra) are also accepted, and can be created using rSDM::locs2vect().

Default map with occmap

Unless a raster ras is provided, occmap will automatically download a background map from the internet.

occmap(locs, psize = 6)

The background map can be easily changed using the bg argument:

occmap(locs, psize = 6, bg = "CartoDB.Positron")

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

Let's create some new coordinates (e.g. for a different species):

new.locs <- data.frame(lon = c(-5.8, -5.4), lat = c(36.2, 36.5))
new.locs.sf <- locs2sf(new.locs, crs = 4326)

Using 'base' maps

Note the add = TRUE argument:

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

Adding points to a previous map (leaflet)

Note the previous map has to be provided (using prev.map argument):

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)

Note the previous map has to be provided (using prev.map argument):

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.