 Analysis of community ecology data in R

David Zelený

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en:hier-agglom_examples_rscript

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 — en:hier-agglom_examples_rscript [2018/04/09 15:23] (current) 2017/05/11 19:42 David Zelený created 2017/05/11 19:42 David Zelený created Line 1: Line 1: + + library (vegan) + data (BCI)  # example using Baro Colorado data + BCI.log <- log1p (BCI)  # first, log transform species data, which contains numbers of individuals + bc.dist <- vegdist (BCI.log, method = '​bray'​) + bc.dist + print (bc.dist, diag = TRUE) + #​install.packages ('​cluster'​) # install if necessary + library (cluster) + clust <- agnes (sqrt (bc.dist), method = '​ward.D2'​) # calculate Ward's algorithm ​ + # on square-rooted Bray-Curtis distances + plot (clust, which = 2) + rect.hclust (clust, 5, border = 1:5) + groups <- cutree (clust, k = 5) + groups ​ + BCI.env <- read.delim ('​https://​raw.githubusercontent.com/​zdealveindy/​anadat-r/​master/​data/​bci.env.txt'​) + plot (UTM.NS ~ UTM.EW, data = BCI.env, pch = groups, cex = 3)  # this is the simple version, only with symbols differentiating individual groups + plot (UTM.NS ~ UTM.EW, data = BCI.env, pch = groups+20, cex = 3, bg = groups, col = '​white'​) # this is more "​colorful"​ option. Note that symbols now are 21 to 25, arguments '​bg'​ and '​col'​ which + + # First, NMDS with Bray-Curtis distances + NMDS <- metaMDS (sqrt (vegdist (BCI.log))) ​ # note that I could use also "NMDS <- metaMDS (sqrt (bc.dist))"​ here + par (mfrow = c(1,2)) # I want to plot both plots into one figure, with two panels in one row + ordiplot (NMDS, type = '​n'​) + points (NMDS, pch = groups, col = groups) + legend ('​topright',​ pch = 1:5, col = 1:5, legend = 1:5) + + # Second, DCA ordination (implicitly using chi-square distance) + DCA <- decorana (BCI.log) + ordiplot (DCA, type = '​n',​ display = '​si'​) + points (DCA, pch = groups, col = groups) + legend ('​topright',​ pch = 1:5, col = 1:5, legend = 1:5,) +
en/hier-agglom_examples_rscript.txt · Last modified: 2018/04/09 15:23 (external edit) 