The sections divide your study area in big blocks, for which you would like specific metrics to be calculated (e.g. residency time, survival, etc.). In the example above, there are three sections: River, Fjord and Sea. The sections must be filled in in the 'Section' column of the spatial.csv file.

When running a migration() analysis, the order of the sections is relevant and represents the order in which you expect your animals will move. By default, actel will order the sections by the order in which they appear in the spatial.csv file. However, you can force a specific order using the section.order argument. For example, if you expect your animals to move from the river to a fjord and ultimately to the sea (and you have receiver arrays in all these sections), then section.order = c("River", "Fjord", "Sea"). In the other hand, if you expect your animals to migrate upstream, then section.order = c("Sea", "Fjord", "River").

For the residency analysis, the order of the sections is not relevant, except for plotting and column order purposes. Like above, actel can sort out the order by itself, or you can specify a specific order using the section.order argument.

The explore() analysis does not take sections into consideration.

If your study area includes multiple pathways that the animals may take, you must tell actel how to connect the arrays. By default, arrays are sorted in a linear order according to the spatial.csv file. To instruct actel to act otherwise, you must create a 'spatial.txt' file. The spatial.txt file is very simple; all you need to do is connect your arrays in pairs. You can learn more about spatial.txt files here.

Now you know how to organise your study area in a way that actel will understand!

Single channel

Let's imagine the following study area, where the red dots represent receiver stations. The first thing you will want to do is give individual names to your stations:

Then, you need to decide how these stations should be organized into arrays. In this case, let's say each station is its own array:

Then, you need to decide how many sections there are in your study area. In this case, one section (e.g. "River") would probably be the best fit, but let's say we have two sections, for the sake of the exercise:

Now that you know your stations, arrays, and sections, you can start filling up the spatial.csv file. Because each array is composed by a single station, you can simply use the station names as array names (avoid using spaces or special characters in array names). Station 'A' will belong to the array 'A', which belongs to section 'Up'; station 'D' belongs to the array 'D' and section 'Down', etc:

Now onwards to the release sites. If you only have one release site at the top of the study area, i.e.:

Then you are sure that the animals are expected to be first detected at array A:

However, you can also have animals released somewhere in the middle of the study area, i.e.:

In this case, if you know that your animals are expected to move in a specific direction (i.e. a migration scenario), then we could say that there is only one expected first array (array D, if the animal is migrating left to right):

However, if you do not know which direction the animals will take (i.e. a residency scenario), then the animal is just as likely to be first detected at array D as it is to be detected at array C. To account for this, you must include both arrays in the spatial.csv file, separating them with a "|".

You can now combine the stations and the release sites to obtain your spatial.csv file:

Complex study area:

Let's now imagine a more complex study area, like the one below:

Like before, you need to name your stations, group them into arrays, and define your study area sections:

We can then start filling in the spatial.csv file:

Now let's assume the animals are released inside the lake:

In this case, regardless of the analysis you are running (migration or residency), there is uncertainty in the first expected array. If you expect that the animals will be migrating from the Lake to the River, you should state that the expected first arrays are either East1 or East2. If you are running a residency analysis, then it may make more sense to consider all Lake arrays as potential first arrays.

So, if you know your animals are moving to the river:

If you don't know where the animals will go to:

Like before, you can now compile the full spatial.csv file:

Since this study area is not linear, you would be required to write a spatial.txt file to tell actel how to link the arrays. You can learn more about spatial.txt files here.