Chapter 5 Change the base map

5.1 Load a realistic map


One parameter of the abstract scenario is the Map Initializer. This controls the basic geography of the scenario. Most applications of POSEIDON will involve loading a map from an external file. Let’s do so here by selecting From File Map as the Map Initializer.

There are 4 parameters to From File Map:

  1. Map File: which is merely the path to the .csv file containing the bathymetry
  2. Grid Width in Cell: this is how many cells in POSEIDON will the csv map be subdivided in. For example, if we leave 100 as default the map will be a grid of width 100 (and the height proportional to the heigth-width ratio of the input).
  3. Header which is true if the csv file has a non numeric first row
  4. Lat Long which is true when the original map’s coordinates are lat-long; when this is false the coordinates are assumed UTM. Lat-long coordinates might result in slightly slower models because the distance function involves a couple of trigonometric functions. However UTM often involves large space distortions.

The Map File is simply a long list of \(x\) and \(y\) coordinates followed by an altitude reading (negative means underwater).

##        x y  depth
## 1 105.04 0 -31.00
## 2 105.13 0 -31.00
## 3 105.22 0 -32.91
## 4 105.31 0 -35.81
## 5 105.40 0 -37.00

POSEIDON will act at a coarser resolution than what is present in the input file. The depth of a cell in POSEIDON will be the average depth of all rows the csv file that are assigned to that POSEIDON cell.

As shown in the video, the inputs folder in POSEIDON already contains some csv files. Here we are going to open inputs/indonesia/small_712_map.csv. This is centered around WPP712 (north of the island of Java) in Indonesia.

The model will then look and run very much like all the other abstract runs (including its own fishing front) but within the map currently generated.

5.2 Download other maps

There are of course many ways to find maps from GIS sources such as here. Most of these data sets are tif rasters that need to be converted (and sometimes they need to be reprojected as well).
The quickest way to get a map into POSEIDON is probably by querying bathymetry from OCTOPUS, a great tool from Marc Weiland when he was at Oxford’s zoology department.

Imagine wanting depth data in lat-long coordinates for the area between the points (105,-15) and (139,5). Simply copy paste the following address to your browser (or wget): &request=GetCoverage &format=geotiff &coverage=context:depth_none_009_gebco &bbox=105,-15,139,5 &crs=EPSG:4326 &resx=0.09 &resy=0.09
Pay particular attention to bbox which is where coordinates are set.

This will download a geotiff file with the correct lat-long projection(EPSG:4326). We can turn it into csv in R easily, with something like this:

Ready to go!