# class exercises 

#  using the dune and dune.env data sets
#  these are 30 species, 20 sites of meadow vegetation on
#    the island of Terschelling in the Netherlands
#  Terschelling is a barrier island in the North Sea

#  species acronyms are provided.  The sites are numbered.
#  The environmental data include:
#    A1: thickness of A1 horizon
#    moisture content: ordered factor
#    managament: Biological Farming, Hobby Farming, 
#      Nature conservation Management, and Standard Farming
#    use: Hayfield, HayPasture, Pasture
#    manure: amount of manure (fertilizer) applied

# the data were collected to examine the relationship between
#   management and species composition

# the species abundance is recorded on an ordinal Braun-Blanquet scale
#   (a detail you don't need to worry about, unless you wonder what
#    the values "mean").
# I suggest Bray-Curtis distance without any transformation 


# the data are available in vegan:

library(vegan)
data(dune)
data(dune.env)

dim(dune)
names(dune.env)

# what can you say about the effect of management (the Management variable)
#   on species composition?

# if you explore the data, you may notice that soil moisture is strongly
#   associated with species composition

# if you control for differences in soil moisture, what can you say about
#   the effect of management on species composition?