Skip to content
Prev 6618 / 7419 Next

Question regarding Bray Curtis and NMDS

Hello,
I was recommended this email by another student for R help;
I am currently analyzing differences in fish assemblages due to temperature
extremes. I am looking at data over multiple years.
I chose three sampling sites within a single bay, the sites are used as
replicates for my analysis. The ultimate goal would be to determine if
there is any difference between assemblages in a given year and is it the
significant difference occurring between a warm and cold year.
 I am interested in determining if the assemblages have a significant
difference between species in the the years, thus I am looking to use Bray
Curtis dissimilarity and displaying it in NMDS.
I want to use the transformed Bray-Curtis for NMDS rather than Hellinger
transformation but it is not displaying properly as Bray Curtis will only
display the years not the species names in the matrix.  I am fairly new to
vegan and multivariate analysis.
Thank you for your time and help,
Data Code:
#Packages
library(vegan)
library(ggvegan)
library(ggplot2)
library(tidyverse)
#4th root transformation for count data
 >BBcounts_transformed<-siteBB^(1/4)
#Bray-Curtis analysis
 >BBtrans_bray<-vegdist(BBcounts_transformed, method="bray")

Wish to replace with hellinger transformation for this given code:
#NMDS-unconstrained
#Transform using Hellinger
#Fortify graphing
geom_point(data=subset(fort_BB, Score =='sites'),
             mapping = aes(x = NMDS1, y = NMDS2),
             color="black",
             alpha=0.5) +
  geom_segment(data=subset(fort_BB,Score == 'species'),
               mapping=aes(x=0,y=0,xend=NMDS1,yend=NMDS2),
               arrow=arrow(length = unit(0.015,"npc"),
                           type="closed"),
               color="darkgrey",
               size=0.8) +
  geom_text(data=subset(fort_BB, Score == 'species'),
            mapping=aes(label=Label, x= NMDS1 * 1.3, y= NMDS2 *1.3))+
  geom_abline(intercept=0,slope=0,linetype="dashed", size=0.8,
color="gray") +
  geom_vline(aes(xintercept=0), linetype="dashed", size=0.8, color="gray") +
  theme(panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        panel.background = element_blank(),
        axis.line=element_line(color="black")