rawMatrix<-read.csv("tubes.csv",row.names=1,h=T,na.strings="?")


dataMatrix<-rawMatrix[c(-1,-2,-3,-4)]

distanceMatrix<-daisy(dataMatrix,metric='gower')

nmds2<-metaMDS(distanceMatrix,trymax=500,k=2,autotransform=FALSE)

nmds3<-metaMDS(distanceMatrix,trymax=500,k=3,autotransform=FALSE) 

nmds4<-metaMDS(distanceMatrix,trymax=500,k=4,autotransform=FALSE)
 
nmds5<-metaMDS(distanceMatrix,trymax=500,k=5,autotransform=FALSE)
 
nmds6<-metaMDS(distanceMatrix,trymax=500,k=6,autotransform=FALSE)
 
nmds2
nmds3
nmds4
nmds5
nmds6

dm<-as.matrix(distanceMatrix)
dimcheckMDS(dm,distance="gower",k=6,trymax=200,autotransform=FALSE)

type<-as.character(rawMatrix[,1])
type2<-as.character(rawMatrix[,2])
type3<-as.character(rawMatrix[,3])

cols<-as.character(rawMatrix[,4])
plot(nmds3,type='n',xlab="NMDS Axis 1",ylab="NMDS Axis 2")
with(rawMatrix,points(nmds3,display='sites',col=cols,pch=20)) 
text(nmds3,display='sites',cex=0.6, pos=4)
ordihull(nmds3,type3,draw='polygon',col=cols,lwd=0.5)

ordihull(nmds3,type,draw='polygon',col=cols,lwd=0.5)

groupEdia<-as.matrix(subset(rawMatrix,rawMatrix[,1]=="Ediacaran"))
groupCam<-as.matrix(subset(rawMatrix,rawMatrix[,1]=="Camrbian"))
groupEdiaAu<-as.matrix(subset(rawMatrix,rawMatrix[,2]=="Ediacaran"))

Edia<-dplyr::filter(rawMatrix,rawMatrix[,1]=="Ediacaran")
Ediar<-rownames_to_column(Edia, var = "rowname")
Ediacaran<-Ediar$rowname

Camb<-dplyr::filter(rawMatrix,rawMatrix[,2]=="Camrbian")
Cambr<-rownames_to_column(Camb, var = "rowname")
Cambrian<-Cambr$rowname

EdiaA<-dplyr::filter(rawMatrix,rawMatrix[,2]=="Ediacaran")
EdiaAr<-rownames_to_column(EdiaA, var = "rowname")
EdiacaranAurora<-EdiaAr$rowname

Au<-dplyr::filter(rawMatrix,rawMatrix[,4]=="black")
Aur<-rownames_to_column(Au, var = "rowname")
Aurora<-Aur$rowname


dm<-as.matrix(distanceMatrix) 
sub<-custom.subsets(dm,list("Ediacaran"=Ediacaran, "Ediacaran+Auroralumina"=EdiacaranAurora,"Cambrian"=Cambrian))
eac<-custom.subsets(dm,list("Ediacaran+Auroralumina"=EdiacaranAurora,"Cambrian"=Cambrian))
eea<-custom.subsets(dm,list("Ediacaran"=Ediacaran, "Ediacaran+Auroralumina"=EdiacaranAurora))
ec<-custom.subsets(dm,list("Ediacaran"=Ediacaran, "Cambrian"=Cambrian))

addisp<-adonis.dispRity(sub,method="gower")
addisp

boots<-boot.matrix(sub,bootstraps=100)

sum_of_ranges<-dispRity(boots,metric=c(sum,ranges))
summary(sum_of_ranges)
plot(sum_of_ranges,main="Sum of Ranges")

convol<-dispRity(sub,convhull.volume) ##error - not enough points
plot(convol)

centroids<-dispRity(boots,metric=c(median, centroids))
plot(centroids, main="Median of Centroids")

sum_of_variances<-dispRity(boots, metric=c(sum,variances))
plot(sum_of_variances, main="Sum of Variances")

ave_neighbours<-dispRity(boots, metric = neighbours,which = mean, method = "gower")
plot(ave_neighbours, main="Average Neighbours")

min_neighbours<-dispRity(boots, metric = neighbours,which = min, method = "gower")
plot(min_neighbours, main="Nearest Neighbours")

pair_dist<-dispRity(boots, metric=pairwise.dist, method = "gower")
plot(pair_dist,main = "Pairwise Distances")

gp_dist<-dispRity(boots, metric=group.dist, method = "gower")
plot(gp_dist,main = "Group Distances")