§r §maps §sdm

# Reference

This is an update of my previous mapping tutorial. Spatial analysis in R is shifting to terra and sf as the primary packages, so I’ve translated my old, raster-based tutorial to the new workflow. See the RSpatial tutorial for a more detailed introduction/overview of using terra for GIS/spatial analysis.

The following tutorial walks through some common plotting tasks I use for distribution models.

# Basemaps

The geodata package provides several convenient functions for downloading raster and vector maps for use as basemaps and spatial analysis. The first time you use these functions, they will download the requested maps from the internet. It will save the data in your working directory, or in a location specified with the path argument. The next time you request the same data, if it finds them in the local directory (or the specified path), they will be loaded from there, saving the time and bandwith necessary to download them.

library(geodata)
## Loading required package: terra
## terra 1.7.6
us <- gadm(country = "USA", level = 1, resolution = 2,
path = "../data/maps/")
path = "../data/maps")
mexico <- gadm(country = "MX", level = 1, resolution = 2,
path = "../data/maps")

Countries are specified by their ISO code, which you can find by calling the function country_codes(). The other arguments allow you to select, national, subnational, or subprovnicial borders (level 1-3), the resolution (high: 1, low: 2), and the path to the directory where you want the maps stored.

These maps can be plotted directly with the plot command. If you want to combine them, use the add = TRUE argument to the second plot call:

plot(us, lwd = 2)
plot(mexico, add = TRUE, border = "green")

col sets the fill colour, border sets the outline color.

You can also request multiple countries as a single set of polygons, by passing a character vector to the country argument.

NorthAmerica <- gadm(country = c("USA", "CAN", "MX"),
level = 0, resolution = 2,
path = "../data/maps/")

plot(NorthAmerica, xlim = c(-180, -50))

Note that xlim and ylim work as you would expect for plotting.

If you want to combine multiple polygons into a single object, use rbind:

CanUS <- rbind(us, canada)
plot(CanUS, xlim = c(-180, -50))

These maps are ‘unprojected’, meaning they are plotted in latitude/longitude degrees. That makes it easy to set the plot boundaries:

plot(CanUS, xlim = c(-100, -50), ylim = c(30, 60))
plot(NorthAmerica, lwd = 2, add = TRUE)

NB: The size of your plot canvas is fixed, but a map can’t stretch. The x and y dimensions have to maintain the same aspect. That means zooming in one dimension (i.e. latitude only) won’t necessarily change the zoom of your map, if the other dimension fills the canvas. You’ll have to play around with the plot size, and both x and y dimensions together, to tweak your zoom.

It’s handy to have a shapefile of the Great Lakes, for making prettier maps. I created this one in QGIS and use it for plotting:

greatlakes <- vect("../data/maps/greatlakes.shp")

## Vectors

You can add points to the plot like a regular scatter plot:

library(scales)  ## for the alpha function below
##
## Attaching package: 'scales'
## The following object is masked from 'package:terra':
##
##     rescale
gbif <- read.table("../data/trich-gbif.csv")
## Set the line color to gray to focus on the data points:
plot(CanUS, xlim = c(-100, -50), ylim = c(30, 60),
border = "gray")
points(gbif$X, gbif$Y, pch = 16,
col = alpha("green", 0.2))

You can also convert your points to a spatial vector object, in which case R will know which columns to use for plotting. This is also necessary before we can project our data (see below).

gbif <- vect(gbif, geom = c("X", "Y"))
## plot(CanUS, xlim = c(-100, -50), ylim = c(30, 60),
##      border = "gray")
## points(gbif, pch = 16, col = alpha("green", 0.2))

## Rasters

Similarly, you can plot rasters with plot:

trichPreds <- rast("../data/trichPreds.grd")
plot(trichPreds, xlim = c(-100, -50), ylim = c(30, 60))
plot(CanUS, border = "gray", lwd = 0.5, add = TRUE)

Cells with NA values are transparent. In this case, a species distribution model, low values are displayed in gray. This may be useful for visualizing the extent of the model. However, it looks a bit odd, and makes it hard to see limits of the high-suitability areas. You can tweak this by playing with the color ramp, but it’s also handy to ‘turn off’ the low values entirely (for visualization, not for analysis!!)

trichPredsTrim <- trichPreds
trichPredsTrim[trichPredsTrim <
quantile(values(trichPreds),
probs = 0.75, na.rm = TRUE)] <- NA
plot(trichPredsTrim, xlim = c(-100, -50), ylim = c(30, 60))
plot(CanUS, border = "grey", add = TRUE)

The test I used here, trichPredsTrim < quantile(getValues(trichPreds), probs = 0.75, na.rm = TRUE) identifies all cells in the lower 75% of the suitability scores, which I then set to NA to make them invisible. I decided on 75% after experimenting with different values. In this case, 75% drops most of the grey background (the very lowest values), without eating into the areas that the prediction indicates are suitable.

You could also use an absolute value here, but then you’d need to know the actual distribution of the suitability scores. quantile is easier to tweak.

# Projections

Lat/Lon maps look a bit square; we’re more used to seeing maps projected. A common projection for Canada is Lambert Conformal Conic. We can transform our data to this projection to make nicer maps:

## define the projection
canlam <- "+proj=lcc +lat_1=49 +lat_2=77 +lat_0=49 +lon_0=-95 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs"

## project our vector data:
CanUS.lcc <- project(CanUS, canlam)
gl.lcc <- project(greatlakes, canlam)

## Now we to set the projection of our points:
crs(gbif) <- "+proj=longlat +datum=WGS84"

## Finally, we can project our points to LCC:
gbif.lcc <- project(gbif, canlam)

Note that our data needs to be in an object of class Spat*, and it must have a defined coordinate reference system (CRS) before we can project it to a new CRS. The crs function allows us to explicitly set the projection. See the RSpatial tutorial for more details on specifying CRS with terra.

The same function works for rasters (sort of):

rasterLCC <- project(trichPredsTrim, canlam)

This will reproject my raster from lat/lon to Lambert Conformal Conic, but we will unavoidably lose some precision when we do this. This is fine for visualization, but you should avoid projecting raster data used in analysis. For more details, see the terra tutorial.

plot(rasterLCC)
plot(CanUS.lcc, border = "grey", add = TRUE)

The units are no longer Lat/Lon, but meters. We can read them off the plot to improve the zoom:

plot(rasterLCC, xlim = c(0, 2500000),
ylim = c(-1500000, -400000))
plot(CanUS.lcc, border = "grey", add = TRUE)

# Formatting

With the data plotted, we can then turn to making the map a little prettier. Note that when working with Spat* objects, we can’t set the plot margins with par as we usually do. Instead, we use the mar argument within the plot function:

## Make a panel with two plots
par(mfrow = c(1, 2))

## store the plot limits:
my_xlims <- c(0, 2500000)
my_ylims <- c(-1300000, -200000)

## Plot the points:
plot(CanUS.lcc, xlim = my_xlims , ylim = my_ylims,
border = "grey", background = "lightblue",
col = "white", axes = FALSE, mar = c(0.1,0.1,0.1,0))
plot(gl.lcc, add = TRUE, border = "grey", col = "lightblue")
points(gbif.lcc, pch = 16, col = alpha("grey30", 0.2),
cex = 0.7)
box()

plot(CanUS.lcc, xlim = my_xlims , ylim = my_ylims,
border = "grey", background = "lightblue",
col = "white", mar = c(0.1,0,0.1,0.1), axes = FALSE)
plot(gl.lcc, add = TRUE, border = "grey", col = "lightblue")
plot(rasterLCC, add = TRUE, legend = FALSE, axes = FALSE)

## plotted again to put the border lines on top:
plot(CanUS.lcc, border = "grey", add = TRUE)
box()

If you want to plot the state/provincial borders on top of the raster, you need to add those layers last. But you can’t set the background colour of the raster layer to “lightblue” (or at least I haven’t figured that out), so the ocean stays white. I get around that by plotting the boundaries twice, first to set the background colour, and then to put the state lines on top of the raster.