#R Scripts to produce analyses for Beta-Diversity on Deep-Sea Wood Falls Reflects Gradients in Energy Availability # Craig McClain and James Barry, Biology Letters #change working directory setwd("/Directory") wood_data=read.csv("woodfall_species.csv") #load data for wood falls ans species list wood_data[is.na(wood_data)]<-0 ###change na's to zeros attach(wood_data) row.names(wood_data)<-wood_data$Log wood_species=data.frame(Xylophaga.zierenbergi,Xylophaga.concava, Gastropod.1,Gastropod.2,Gastropod.3,Gastropod.4,Gastropod.5, Gastropod.7, Limpet,Anemone_sm, Anemone_lg, Crinoid1, Crinooid, Ophiuroid, Bivalve, Poly1, Poly2, Poly3, Poly4, Poly6, Poly7, Poly8, Poly9, Poly10, Poly11, Tanaid1, Amphi1, Amphi2, Galatheid) row.names(wood_species)<-wood_data$Log #MDS and CAP analysis ################################################################################################ library(vegan) wood_ord<-metaMDS(wood_species) summary(wood_ord) ##fitting environmental variables ord.fit <- envfit(wood_ord ~ Weight..kg. + Halo, data=wood_species, perm=1000) ord.fit ##MDS Plot For Figure 1 plot(wood_ord, disp="sites", type="n") ordispider(wood_ord, Halo, col="black", label = TRUE) points(wood_ord, disp="sites", pch=21, col="black", bg="steelblue2", cex=1.3) plot(ord.fit) #add wood weights in ordisurf(wood_ord, Weight..kg., add=TRUE, col="saddlebrown") ###CAP dbRDA_wood<-capscale(wood_species~Weight..kg.+Halo+Surface.Area..cm2., data=wood_species) dbRDA_wood plot(dbRDA_wood) #plot for Figure 2 anova(dbRDA_wood, by="term", permu=10000) #testing for differences in community structure realted to distance between wood falls ################################################################################################ wood.dist<-vegdist(wood_species) coordinates<-data.frame(X,Y) real.dist<-vegdist(coordinates, "euclid") mantel(wood.dist,real.dist, method="spear")