Our next R course is at University of Queensland (Australia) from 11th Feburary 2020. Beginner, intermediate and advanced classes available.
I’m loving the
tmap package right now. Here’s why. And we’ll look at
how to make a clean map of a study site as we go.
sf (‘Simple Features’) is the new spatial data standard for R.
Let’s create an sf points file. First we’ll read the data from the github repo
sites <- read.csv(url("https://raw.githubusercontent.com/cbrown5/BenthicLatent/master/data-raw/JuvUVCSites_with_ReefTypes_16Jun2016.csv"))
Its a list of dive sites, where reef type, coral cover and some other variables were observed.
(So grateful for Rick Hamilton for letting me make this data open access. Just remember, there are a lot of crocodiles in the Solomon Islands, diving in and around mangroves to collect data like this isn’t the easiest job)
Now to make an sf object:
library(sf) ## Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3 sites <- st_as_sf(sites, coords = c("coordx", "coordy"))
Let’s also get the land for context (you can download this folder from the github repo)
land <- st_read(dsn ="LandPoly")
Finally, the points have the same coordinate reference system as the polygon, so add that onto the points:
st_crs(sites) <- st_crs(land)
Maps are just a series of layers. So lets plot the land (using tmap) first:
library(tmap) tm_shape(land) + tm_polygons()
To plot a layer in
tmap you say
tm_shape(data_file_name) first then
add the type of layer you want to plot (like
Now we will also want to add on the points (dive sites) layer. We can
tm_symbols for this:
tm_shape(land) + tm_polygons() + tm_shape(sites)+ tm_symbols(size = 0.5)
I mean the code for cartography is easy. Good cartography is hard (but a good place to start is the book ‘How to Lie with Maps’).
Now let’s keep adding on layers to make our map look nice. It’s all pretty self explanatory once you understand the layering concept:
tm1 <- tm_shape(land) + tm_fill(col = "wheat") + tm_shape(sites)+ tm_symbols(size = 0.3, col = "cover", title.col = "Coral cover", palette = "Reds") + tm_compass(type = "4star", position = c(0.01, 0.67), size = 1.5) + #positions are between 0 & 1 and place the #bottom left corner tm_scale_bar(breaks = c(0, 10), position = c(0.65, 0.01), text.size = 0.6) + tm_layout(legend.position = c("right", "top"), legend.title.size = 0.8, bg.color = "lightblue") + tm_credits("Study sites from \nBrown and Hamilton 2018 \nConservation Biology. \nCoastline derived from Landsat.", size = 0.7, position = c(0.01, 0.01)) tm1
You might have to play around with the position adjustments for a while to get everything placed just right.
Finally, you can save your map to file
tmap_save(tm1, filename = "mymap.png", width = 8, height = 8)