# TWINSPAN in R applied on Danube dataset

# Install the twinspanR library from GitHub repository:
install.packages ('devtools')
devtools::install_github("zdealveindy/twinspanR")

# initiate the library and data
library (twinspanR)
data (danube)
?danube

# calculates standard twispan, with default setting
tw <- twinspan (danube$spe, modif = F)

# cuts the results into vector of sample assignments to groups
tw.groups <- cut (tw, cluster = 4)

# Calculates and draws the DCA ordination diagram
DCA <- decorana (log1p (danube$spe))
plot (DCA, display = 'sites', type = 'n')
points (DCA, col = tw.groups)
ordihull (DCA, groups = tw.groups)
plot (envfit (DCA, danube$env[,1:3]))

# Prints the two-way ordered table from twinspan
print (tw, 'table')