#Partial RDA
mite.spe.subs=rda(mite.spe.hel ~ Shrub + Topo
                  + Condition(SubsDens + WatrCont + Substrate), data=mite.env)
 
#Summary
summary(mite.spe.subs, display=NULL)
(R2adj <- RsquareAdj(mite.spe.subs)$adj.r.squared)
 
#Significant axes
anova.cca(mite.spe.subs, step=1000)
anova.cca(mite.spe.subs, step=1000, by="axis")
 
#Triplot scaling 1
windows(title="Partial RDA scaling 1")
plot(mite.spe.subs, scaling=1, main="Triplot partial RDA - scaling 1", type="none", xlab=c("RDA1"), ylab=c("RDA2"), xlim=c(-1,1), ylim=c(-1,1))
points(scores(mite.spe.subs, display="sites", choices=c(1,2), scaling=1),
       pch=21, col="black", bg="steelblue", cex=1.2)
arrows(0,0,
       scores(mite.spe.subs, display="species", choices=c(1), scaling=1),
       scores(mite.spe.subs, display="species", choices=c(2), scaling=1),
       col="black",length=0)
text(scores(mite.spe.subs, display="species", choices=c(1), scaling=1),
     scores(mite.spe.subs, display="species", choices=c(2), scaling=1),
     labels=rownames(scores(mite.spe.subs, display="species", scaling=1)),
     col="black", cex=0.8)  
arrows(0,0,
       scores(mite.spe.subs, display="bp", choices=c(1), scaling=1),
       scores(mite.spe.subs, display="bp", choices=c(2), scaling=1),
       col="red")
text(scores(mite.spe.subs, display="bp", choices=c(1), scaling=1)+0.05,
     scores(mite.spe.subs, display="bp", choices=c(2), scaling=1)+0.05,
     labels=rownames(scores(mite.spe.subs, display="bp", choices=c(2), scaling=1)),
     col="red", cex=1) 
 
#Triplot scaling 2
windows(title="Partial RDA scaling 2")
plot(mite.spe.subs, scaling=2, main="Triplot partial RDA - scaling 2", type="none", xlab=c("RDA1"), ylab=c("RDA2"), xlim=c(-1,1), ylim=c(-1,1))
points(scores(mite.spe.subs, display="sites", choices=c(1,2), scaling=2),
       pch=21, col="black", bg="steelblue", cex=1.2)
arrows(0,0,
       scores(mite.spe.subs, display="species", choices=c(1), scaling=2),
       scores(mite.spe.subs, display="species", choices=c(2), scaling=2),
       col="black",length=0)
text(scores(mite.spe.subs, display="species", choices=c(1), scaling=2),
     scores(mite.spe.subs, display="species", choices=c(2), scaling=2),
     labels=rownames(scores(mite.spe.subs, display="species", scaling=2)),
     col="black", cex=0.8)  
arrows(0,0,
       scores(mite.spe.subs, display="bp", choices=c(1), scaling=2),
       scores(mite.spe.subs, display="bp", choices=c(2), scaling=2),
       col="red")
text(scores(mite.spe.subs, display="bp", choices=c(1), scaling=2)+0.05,
     scores(mite.spe.subs, display="bp", choices=c(2), scaling=2)+0.05,
     labels=rownames(scores(mite.spe.subs, display="bp", choices=c(2), scaling=2)),
     col="red", cex=1)