# Twinspan nefunguje
devtools::install_github("jarioksa/twinspan")
install.packages("twinspan", repos="https://jarioksa.github.io/drat/")

### Isopam
library(isopam)
library(vegan)
library(cluster)


#
vin<-read.csv("vineyards.csv", row.names=1)
summary(vin)

table(colSums(vin>0)>1)
vin.2<-vin[,colSums(vin>0)>1]

iso.1<-isopam(sqrt(vin.2), c.max=3, l.max=3, sieve=F)

plot(iso.1)
iso.1$flat

iso.1$flat$level.2

aa<-isotab(iso.1, level=2, phi.min = 0.3)
print(aa)

pco.1<-capscale(sqrt(vin.2)~1, distance = "bray", sqrt.dist = T)
bb<-ordiplot(pco.1, type="n", display="si",
                choices=c(1,2))
points(bb, what="si", col=iso.1$flat$level.2, pch=16, cex=0.6)
ordispider(pco.1, groups=iso.1$flat$level.2, pch=16, cex=0.6,
           col=1:4)

plot(silhouette(iso.1$flat$level.2, vegdist(
  sqrt(vin.2), method="bray")))

### Data Petra Hubatky

iso.2<-isopam(sqrt(jedno.2), c.max=4, l.max=2, sieve=T)
plot(iso.2)

iso.2$flat
plot(silhouette(iso.2$flat$level.2, vegdist(
  sqrt(jedno.2), method="bray")))

aa<-isotab(iso.2, level=2, phi.min=0.3)

pco.1<-capscale(sqrt(jedno.2)~1, distance = "bray", sqrt.dist = T)
bb<-ordiplot(pco.1, type="n", display="si",
                choices=c(1,2))
points(bb, what="si", col=iso.2$flat$level.2, pch=16, cex=0.6)
ordispider(pco.1, groups=iso.2$flat$level.2, pch=16, cex=0.6,
           col=1:4)