nonmetric multidimensional scaling (nmds) ordi.DOCXVIP

Nonmetric Multidimensional Scaling (NMDS) OrdinationVegan package in RKatherine HovanesBIOL 7901 – R seminar – Spring 2013Nonmetric Multidimensional Scaling ordination can be used to plot samples in “ecological space” using a community dissimilarity matrix based on species composition. Communities that have very similar species composition will appear as points near each other whereas communities that have very different species compositions will be further away from each other on the plot. Points can be color coded by categorical factors so you can see the grouping of samples based on categorical environmental factors. In order to determine whether samples are “significantly” different by one of the categorical environmental factors you can perform a permutational ANOVA (PERMANOVA) on your presence/absence matrix. I will cover NMDS ordination using the function “metaMDS” (packages vegan and MASS required). Plots of the ordination will be done with the plot function and “ordisymbol” (from package BiodiversityR). The PERMANOVA test is done with the function “adonis” (from vegan). The dataset “KNF_mod.txt” is the groundcover vegetation species composition of 89 1-m2 plots in the Kisatchie National Forest; this has been modified from the original dataset, so it isn’t “real” data, just something to play with for this tutorial.There is much more to the vegan package than ordination. Check out this source to see all of the functions in vegan: /web/packages/vegan/vegan.pdf/web/packages/vegan/vegan.pdfFirst load the necessary libraries; make sure you have downloaded and installed vegan, BiodiversityR, and MASS. #libraries library(vegan) library(BiodiversityR) library(MASS)Now read in the data and check the first few rows and columns. You’ll see that the first 5 columns are categorical data about each plot (plot #, soil type, slope position, fire season, and presence vs. absence of the dominant bunchgrass Schizachyrium scoparium). The presence/absence matrix of sp