ALGORITHM-dev: DynComm Documentation for Developers of new Main Algorithms
In DynComm: Dynamic Network Communities Detection and Generation

Instructions for adding new main algorithms to the DynComm package.

This section provides step by step instructions on how to implement a new main algorithm and how to integrate it into the DynComm package.

Go to the project source and get an appropriate template for your algorithm from the "dev" folder on the root of the project source.
Different languages are distinguished by the extension of the file.
If a template is not available use one from a language that is most related to the language you intend to use or use the R template to, at least, provide you with the function names, types of inputs and types of outputs.
Implement the new algorithm inside the template, preferably, inside a private function. The algorithm, that is the private function, must be called at the end of the addRemoveVertices function of the API.
All functions, except the addRemoveVertices, must only be used to convert between data types and to return data. No calculations should be performed in them.

R

Temporarily add any library required by the algorithm in your source file. It will have to be removed later but, for now, it is useful for testing.

Depending on the programming language used, do the following:

R

Choose the "TemplateDynCommMain.R" template.
Save the source file of the new algorithm in the "R-CRAN/R" folder.

C++11

Choose the "TemplateDynCommMain.h" template.
Save the source file of the new algorithm in the "R-CRAN/src/base/Cpp" folder.

Python

Choose the "TemplateDynCommMain.py" template.
Save the source file of the new algorithm in the "R-CRAN/src/base/Python" folder.

The name of the file should reflect the name of the algorithm and start with the word "algorithm".
Test the algorithm independently of the DynComm package. If programming in...

R

You can "source" your R file.

C++11

You might have to write a small program to test it, that can later be used to produce a standalone version. Or you can integrate it in the existing C++ standalone, modifying where needed.
If you want to use the existing standalone to test your algorithm, the file is named "DynCommEXE.cpp". Follow the instructions in its developer notice.
Continue to read these instructions to know how to integrate your code into the existing C++ source code. The steps are identical to the integration of your algorithm into this package except that you can skip the documentation and editing of any R files.
Afterwards, you can resume reading from here to implement the missing steps to integrate into this package.

Python

You can test it by invoking it directly from a python command line. Check Python documentation on how to do it.

Use the tests performed as examples and write them in the documentation when it is created.
If the algorithm you are creating has associated bibliography, add reference to it in the existing "REFERENCES.bib" file.
Create documentation for your algorithm. This involves adding documentation in three files.
The first is the developer documentation on the same file you implemented your algorithm. If using a template, there is already a documentation template for you to modify.
This documentation must have a detailed description of the algorithm, including a description of how it works, its parameters and contain examples that can be used for automatic testing.
The second file is the "ALGORITHM.R" where the user friendly documentation is written. This documentation should have a high level description of the algorithm, acceptable parameters and supported criterion.
The thrird file is the "DynCommMain.R" where it says "document new algorithms here". This documentation should use the same format used for other algorithms with a very small description of the algorithm, preferably just two lines, with a link to the user friendly documentation and references to publications.
Add the name of your algorithm to the ALGORITHM list in the "DynCommMain.R" file under the marker that says "list new algorithms here".
Add your algorithm parameters to the matrix in the "DynComm.R" file under the marker that says "add parameters here".

R

Add a source command to the "DynCommMain.R" file under the marker that says "Include R sources here". Add any R libraries required by your algorithm to the "DynComm.R" file under the marker that says "List imports here".
Remove all libraries from your algorithms' R source file.

C++11

Edit the file "algorithm.h" and look for the several "...new algorithms here" markers. They will tell what needs to be done to integrate your algorithm.
Then, if your algorithm requires any parameters, edit the file "program.h" and look for the several "...new algorithms here" markers. They will tell what needs to be done to add your algorithms' parameters to the C++ source.

Python

TO DO :(
You should now be able to build the package and, if everything went right, your algorithm is successfuly integrated into this package. Congratulations :D