Edited following helpful feedback.
I have vegetation species data for a number of grassland habitat sites, and am preparing to begin Exploratory Data Analysis.
Data was collected in 100 quadrats over 9 sites in percent cover to attempt to establish one or more species which indicate improved quality of grasslands over time through their presence or abundance (%).
Quadrat Site Soil.type Mean.quadrat.height.cm Species.1% Species.2% Species.3%... 1 2 3 40 5 10 25 2 3 2 50 0 0 10 3 2 1 25 10 0 0
I am confident in the steps I need to take to ensure rigorous data analysis, and I'm not attempting to shirk any long winded jobs, but I wanted to see if I should be reducing the number of species variables before going further. I have over 100 separate species, some of which only occur on one occasion. Certain papers I have seen recommend removing any species which only occur in <5% of quadrats, but I don't know how to back this up. To be on the safe side should I conduct EDA (boxplots etc.) on every single variable, or is there a robust method of species reduction? I had originally thought PCA should do the trick but some literature I have read says other forms of EDA should come before PCA.