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Multilayer #4

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Multilayer #4

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fnobregasantos
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Review Multialyer - Networks code

@@ -0,0 +1 @@
This folder includes all scripts for the Multilayer analysis . All instructions will be found here!
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I would recommend, at some point, writing in more detail a tutorial explaining these analyses/scripts.

I corrected a few typos but mainly changed the style following PEP8 suggestions
The original code uses as input a 3d array, i.e., two variables for the shape of the supra-adjacency matrix and one variable for the number of matrixes. If we have a single supra-adjacency matrix, we often represent it as a 2d array, which would yield a bug in our code.  Although the original code was not wrong, we decided to facilitate the user experience by adapting the code to accept a single supra-adjacency matrix as a 2d array as input. When that happens, the number of individuals in the analysis will be assigned one in the code.
The original code uses as input a 3d array, i.e., two variables for the shape of the supra-adjacency matrix and one variable for the number of matrixes. If we have a single supra-adjacency matrix, we often represent it as a 2d array, which would yield a bug in our code.  Although the original code was not wrong, we decided to facilitate the user experience by adapting the code to accept a single supra-adjacency matrix as a 2d array as input. When that happens, the number of individuals in the analysis will be assigned one in the code.
@multinetlab multinetlab linked an issue Dec 23, 2021 that may be closed by this pull request
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@fnobregasantos @lcbreedt Before your next commit, please have a look at the files in the repo and check which should be kept. There's one code outside the Multilayer folder, and another one inside.

We commented that you should always start with 0 as the first layer, not 1 (like in other programs such as Matlab).
Included example to path similar to the one described by Marika
Including a reminder to subtract -1 from your subnetwork list
Reminder for a path to output file
This code was a user file before the previous commit. It was wrongly overwritten with the Multilayer main code. This commit is only reverting it.
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adapt MULTILAYER according to feedback.
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