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Our next R course is at University of Queensland (Australia) from 11th Feburary 2020. Beginner, intermediate and advanced classes available.

seascape models

Make a map of your study site with tmap

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.

We’ll use the data from our study of pollution and coral reefs in the Solmon Islands (repo is here).

It runs smoothly with sf

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)

You build maps as layers like in ggplot

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 ggplot geoms).

Now we will also want to add on the points (dive sites) layer. We can use tm_dots or tm_symbols for this:

tm_shape(land) +
  tm_polygons() +
  tm_shape(sites)+
  tm_symbols(size = 0.5)

Cartography is easy

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)

Have fun mapping. For more help see tmap basics or the book Geocomputation with R or come to our course in Queensland February 2018.



Contact: Chris Brown

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Designed by Chris Brown. Source on Github