This code was created to find communities of phytoplankton pigments (measured with High Performance Liquid Chromatography [HPLC]) using network-based community detection methods.
All code and data in this repository are freely available for use by anyone for any and all applications. If you use this code, we ask that you please cite the following paper where these methods were used:
Kramer, S.J., D.A. Siegel, and J.R. Graff (2020). Phytoplankton community composition determined from co-variability among phytoplankton pigments from the NAAMES field campaign. Frontiers in Marine Science, 7(215), 1-15, https://doi.org/10.3389/fmars.2020.00215.
And please also cite the authors of the method(s) that you use in your published analysis:
(1) WGCNA: Zhang, B., and S. Horvath (2005), A general framework for Weighted Gene Co-Expression Network Analysis, Statistical Applications in Genetics and Molecular Biology, 4(1), 1-45, doi:10.2202/1544-6115.1128.
(2) Brain connectivity toolbox: Rubinov, M., and O. Sporns (2010), Complex network measures of brain connectivity: Uses and interpretations, NeuroImage, 52(3), doi:10.1016/j.neuroimage.2009.10.003.
(3) GenLouvain functions: Lucas G. S. Jeub, Marya Bazzi, Inderjit S. Jutla, and Peter J. Mucha, "A generalized Louvain method for community detection implemented in MATLAB," http://netwiki.amath.unc.edu/GenLouvain, https://github.com/GenLouvain/GenLouvain (2011-2019).
Please notify me if you find errors and/or inaccuracies or if you have any questions.