#2
summary(doubs.spe)

#3
library(vegan)

pca.1<-rda(decostand(doubs.spe[,-1], method="hell"))

#4
pca.1

#5
screeplot(pca.1, bstick=T)
abline(h=mean(eigenvals(pca.1)))

#6
plot(pca.1)
ordiplot(pca.1)
?ordiplot
?plot.cca

#7
c(0.24913,0.06592,0.04615)/0.5023


ordi.1<-ordiplot(pca.1, type='n', display = c("si", "sp"),
                 scaling=2, ylim=c(-0.7, 0.5),
                 xlab="PC1 (49.6%)", ylab="PC2 (13.1%)")
points(ordi.1, what="si")
text(ordi.1, what="sp", arrows=T)

ordi.2<-ordiplot(pca.1, type='n', display = c("si", "sp"),
                 scaling=2, ylim=c(-0.6, 0.7),
                 xlab="PC1 (49.6%)", ylab="PC3 (9.2%)",
                 choices=c(1,3))
points(ordi.2, what="si")
text(ordi.2, what="sp", arrows=T, cex=0.8)

# 8
summary(bk.env)
library(fastDummies)
hemi.dummy<-dummy_cols(bk.env$hemiparasite)[,-1]
names(hemi.dummy)<-c("MNE", "RAL", "RMA", "RMI")

bk.env.2<-data.frame(bk.env, hemi.dummy)
bk.env.2<-bk.env.2[,-2]

library(psych)
pdf("bk.pairs.pdf", 8,8)
pairs.panels(bk.env.2)
dev.off()

bk.env.3<-bk.env.2
bk.env.3$PMehl3<-log(bk.env.3$PMehl3)
bk.env.3$Na<-log(bk.env.3$Na)
bk.env.3$Mg<-log(bk.env.3$Mg)
bk.env.3$Ca<-log(bk.env.3$Ca)

pdf("bk.pairs.2.pdf", 8,8)
pairs.panels(bk.env.3)
dev.off()

pca.bk<-rda(bk.env.3, scale=T)
pca.bk

screeplot(pca.bk, bstick=T)

bk.op.1<-ordiplot(pca.bk, scaling=3, type="n",
            ylim=c(-1.5, 1.5)
            )
points(bk.op.1, what="si")
text(bk.op.1, what="sp", arrows=T)

bk.op.2<-ordiplot(pca.bk, scaling=3, type="n",
            ylim=c(-1.5, 1.5), choices=c(1,3))
            
points(bk.op.2, what="si")
text(bk.op.2, what="sp", arrows=T)