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The following data are the abundances of 3 species of gastropods in 5 quadrats (ranging from high shore marsh, Quadrat 1, to low shore marsh, Quadrat 5) in a saltmarsh.
Open the gastropod data file. Note the format of the file, with variables in columns and samples/sites in rows.
The following example is designed to help you appreciate the link between distance measures and ordination space (MDS). The data set consists of distances (km) between major Australia cities (as the crow flies), and is in the form of a triangular matrix.
Open the austcities data file. Note the format of the file, it is a triangular distance matrix.
While the file is a distance matrix, at this stage R is unaware of it, we must manually make it aware (a round about way of saying that we must type a command to force R to treat the data set as a distance matrix. We do this by typing the following command in the top window (Script Window) of R Commander (actually we could alternatively type it on the command prompt of RGui). aust.cities.dis <- as.dist(aust.cities) where aust.cities is the name you gave the Australian cities data set when you imported it, as.dist is the name of the function that forces a data set to be considered a distance matrix, and aust.cities.dis is a new name that I am defining to store the distance matrix. If you chose to enter the statement in the R Commander command log window, once you have completed typing the above statement, press the Submit button in the top right hand corner of R Commander. This will case the statement to be evaluated and the task to be completed.
We are now ready to perform the MDS for the purpose of examining the ordination plot.
A fish ecologist investigated differences in fish community composition associated with flow regulation in rivers of four major New South Wales catchements (Murray, Darling, North Coast and South Coast). A subset of the community data is presented in the file riverfish.csv.
Open the riverfish data file.
Of course, we could explore the patterns amongst sites according to each separate fish species. However, in the full investigation, the fish ecologist had 51 species of freshwater fish, each of which yield slightly different patterns. Furthermore, the fish ecologist was not interested in the patterns of any one species of fish. What he was interested in was whether (and how) the fish communities differed between catchements and flow regimes. Consequently, an MDS was used to explore the patterns amongst sites based on all the fish species.
Ludwig and Reynolds (1988) described a data set in which a number of sites where characterized by the abundances of five species of cockroach.
Open the Ludwig data file.