Distance not calculated for all station of River Gudena (Denmark)

[damianooldoni]

From @PieterjanVerhelst 's comment https://github.com/inbo/fish-tracking/issues/62#issuecomment-721046437:

For the River Gudena the code only calculates distances between some stations

I had to create the line-shapefile myself. For the River Gudena, I added the last part of the river (the original shapefile did not run to the sea)

[damianooldoni]

I am checking this. I found a small bug in function adapt.binarymask(), which is used to extend the raster to include receivers out of the rasterized river by introducing patches.

The error mentioned by @PieterjanVerhelst is generated in this line:

patchCells <- patchCells[sort.list(patchCells[, 2]), ]

If patchCells contains one patch only (see below):

while if more patches are present:

So, sorting by second column (sum) in first case is not possible as there is no second column. This seems not arising an error, but has as consequence that patchCells becomes NULL and no extensions are computed.

A easy-to-solve bug.

[damianooldoni]

Now, after solving the bug described above, it seems that extending the binary mask to get all receivers is taking ages. First I thought it was the problem of the bug which is not a bug actually, then I thought it was due to receivers way too far from the river (via mapview(study.area) + mapview(location.receivers)), sometimes 3km far: @PieterjanVerhelst : I remove this from calculation. However, the problem remains. There is still something wrong in the extension process. I will investigate further.

[PieterjanVerhelst]

@damianooldoni that southern point is indeed 3 km from the Gudena River, but it is in the Lillea river (rivers_id = 22) which is also in the shapefile.

[damianooldoni]

Well, then you have to remove line

gudena <- gudena[gudena$rivers_id == 12,]

[PieterjanVerhelst]

I will subset on both ids instead, otherwise the script will load too many rivers (just to enhance calculation time).

[damianooldoni]

Sure. To do by:

gudena <- gudena[gudena$rivers_id %in% c(12,22),]

Below the result. I recommend you by the way the usage of package mapview and its function mapview() for fast spatial data exploration in RStudio.

[PieterjanVerhelst]

Update: when trying to calculate the distance between stations in the River Gudena, I get the following error:

> control.mask(study.area.binary.extended, locations.receivers)
 Show Traceback

 Rerun with Debug
 Error: length(receivers) not equal to length(matched.receivers) 

Note that it has likely nothing to do with the fact that I created a part of the shapefile myself, since the code runs for other rivers in other countries where I did this as well.

The most up to date code and files are in the branch calculate-distances-various-networks.

[PieterjanVerhelst]

Issue solved in #69