Analysis of community ecology data in R

# PCoA and NMDS ordiagrams using Vltava data (added categorical variable)
 
vltava.spe <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/vltava-spe.txt', row.names = 1)
vltava.env <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/vltava-env.txt')
 
library (vegan)
 
png ('pcoa_nmds.png', width = 8, height = 4, units = 'in', res = 300, pointsize = 11)
par (mfrow = c(1,2))
pcoa <- capscale (log1p (vltava.spe) ~ 1, distance = 'bray', sqrt.dist = TRUE, scaling = 1)
plot (pcoa, main = 'PCoA (MDS)', type = 'n')
points (pcoa, display = 'si', col = vltava.env$GROUP, pch = vltava.env$GROUP)
text (pcoa, display = 'sp', col = "#FF000080", cex = 0.6, scaling = 1, select = colSums (vltava.spe>0)>20)
legend ('bottomleft', pch = 1:4, col = 1:4, legend = 1:4, title = 'GROUP', cex = 0.6)
 
nmds <- metaMDS (log1p (vltava.spe), distance = 'bray', scaling = 1)
plot (nmds, main = 'NMDS', type = 'n', display = 'si')
points (nmds, display = 'si', col = vltava.env$GROUP, pch = vltava.env$GROUP)
text (nmds, display = 'sp', col = "#FF000080", cex = 0.6, select = colSums (vltava.spe>0)>20)
dev.off ()