occmap: Map species occurrences
In Pakillo/rSDM: Species distribution and niche modelling in R

Description Usage Arguments Details Value Examples

View source: R/occmap.R

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

occmap(
  locs,
  ras = NULL,
  bg = "ggmap",
  proj = "+init=epsg:4326",
  pcol = "red",
  alpha = 1,
  psize = 1,
  add = FALSE,
  leaflet.base = NULL,
  mapmisc_server = "maptoolkit",
  filename = "occmap.kmz",
  ...
)

`locs`	A matrix, dataframe, SpatialPoints or SpatialPointsDataFrame containing coordinates of species occurrences. If locs is a matrix or dataframe, it will be converted to a spatial object using `locs2sp`.
`ras`	Raster* object to be used as background for points. Default is NULL, in which case a background map defined by `bg` will be used.
`bg`	Type of background map. Either 'google' for Google maps background (using `gmap`) (note this requires a Google API key - currently not working!), 'coast' for coastlines (using `coastsCoarse` from rworldmap package), 'ggmap' for maps provided by `get_map` in ggmap package, 'leaflet' for an interactive HTML map using leaflet, 'mapmisc' for using any of the layers available in mapmisc package, or 'kml' for producing a KMZ file to be opened with Google Earth.
`proj`	Character string specifying the projection of coordinates data (see `proj4string` or http://spatialreference.org). Default is geographic (unprojected) coordinates, datum WGS84. Not used if locs is already an Spatial object with defined projection.
`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 these occurrences to a previous map? (e.g. for a new species). Default is FALSE. Note this feature doesn't work for all map types. For leaflet maps, when add = TRUE, a leaflet basemap (e.g. as produced by a previous call to occmap) must be provided (see `leaflet.base`).
`leaflet.base`	Leaflet map to be used as basemap to add further points when add is TRUE.
`mapmisc_server`	character. Server/type of background map to be used when bg = "mapmisc". Run `osmTiles` to see all the available layers.
`filename`	Character. Path and filename of the KMZ file produced when bg = "kml".
`...`	additional parameters to be passed to dismo::gmap if bg == 'google' plot if bg == 'coast' ggmap::get_map if bg == 'ggmap' leafletR::leaflet if bg == 'leaflet' raster::plot or raster::plotRGB if bg == 'mapmisc' See these functions help files for details.

If using ggmap and stamen maps, large regions seem to give problems.

A map (plot), unless bg = 'KML' in which case a kmz file is saved to be explored with Google Earth. In some cases, a raster layer, leaflet object, or ggplot object is returned in addition to the map.

## Not run: 
# Using acaule dataset from dismo package:
library(dismo)
data(acaule)

occmap(locs = acaule)  # If 'ras' not provided, default is bg = "ggmap"
occmap(acaule, bg = "coast")  # just coastlines as background map
occmap(acaule, bg = "leaflet") # leaflet interactive map

# Watercolor map from Stamen using ggmap
# NB: use small regions, otherwise give error to download map tiles
locs_redux <- subset(acaule, lon > -80 & lon < -60 & lat > -30 & lat < -10)
occmap(locs = locs_redux, maptype = 'watercolor', source = 'stamen',
           pcol = "darkgreen", psize = 4)

# Plot occurrences in a specific country:
occmap(locs = subset(acaule, country=="Bolivia"), bg = "leaflet")
# (note there are georeferencing errors in the data)


# Add transparency to points
occmap(locs = acaule, pcol = "red", alpha = 0.5, bg = "coast")
occmap(locs = acaule, pcol = "red", alpha = 0.5, bg = "leaflet")


## Providing spatial objects ##
data(meuse)
coordinates(meuse) <- ~x+y
proj4string(meuse) <- CRS("+init=epsg:28992")
occmap(meuse)

#alternatively, provide projection argument:
data(meuse)
coordinates(meuse) <- ~x+y
occmap(meuse, proj = "+init=epsg:28992")

## End(Not run)