This folder contains the R scripts for the checkerboard score (C-score) analysis of non-random species co-occurrence patterns (i.e., species segration and/or aggregation), starting from an abundance table of microbial OTUs/taxa. The abundance table is a tab-delimited text file in which each row represents a microbial entity and each column represents a sampling point (see the example folder).
References:
Ju F, Xia Y, Guo F, Wang ZP, Zhang T. 2014. Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants. Environmental Microbiology. 16(8):2421-2432
Hu AY, Ju F, Hou LY, Li JW, Yang XY, Wang HJ, Mulla SI, Sun Q, Bürgmann H, Yu CP. 2017. Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community. Environmental Microbiology (2017) 19(12), 4993–500
Stone L, Roberts A. 1990. The checkerboard score and species distributions.85(1):74-79. doi: 10.1007/BF00317345.