I am working with a data set on plant presence-absence within 40 plots. For two years, the presence-absence of all plants were noted in each plot. I would now like to investigate whether the plant community is more alike within a given year or within a given plot.
My immediate thought is to run a PCA or other kind of ordination in R. But I am unsure of what kind of PCA/ordination is the most suitable when I have not one, but two grouping variables along with my presence absence data? I have loooked at the PCoA analysis and the MCA analysis. My goal in using the PCA is to give a visual interpretation of potential shift en species within and between plots.
My data has the following structure:
Species 1; Species 2; Species 3; ...; Species n; Year; Plot 1; 0; 1; ...; 1; 2017; 1 0; 0; 1; ...; 0; 2018; 1 1; 1; 1; ...; 1; 2017; 2 1; 0; 0; ...; 1; 2018; 2