## HEADER ####
#
## Project:
# NMDS tutorial following Jeff's approach
#
## Last editor: Ana Natalio
#
## Last edited: 2020.04.01
#
## CONTENTS ####
## 00 Setup
## 01 What's NMDS?
## 02 How does it work?
## 03 Let's do it in R
## 04 References
#
## 00 Setup ####
#
setwd("M:/Stats_Demos/NMDS")
# add here your personal working directory
#
# install.packages("vegan")
#
library(vegan)
#
## 01 What's NMDS? ####
## 02 How does it work? ####
## 03 Let's do it in R ####
#
set.seed(2)
#
community_matrix = matrix(
  sample(1:100, 300, replace = T),
  nrow = 10,
  dimnames = list(paste("community", 1:10, sep = ""),
                  paste("sp", 1:30, sep = "")))
#
example_NMDS = metaMDS(community_matrix, k = 2)
#
stressplot(example_NMDS)
#
plot(example_NMDS)
#
ordiplot(example_NMDS, type = "n")
orditorp(example_NMDS, display = "species", col = "red", air = 0.01)
orditorp(example_NMDS, display = "sites", cex = 1.25, air = 0.01)
#
treat = c(rep("Treatment1", 5), rep("Treatment2", 5))
ordiplot(example_NMDS,type = "n")
ordihull(example_NMDS, groups = treat, draw = "polygon", col = "grey90", label = F)
orditorp(example_NMDS, display = "species", col = "red", air = 0.01)
orditorp(example_NMDS, display = "sites", col = c(rep("green", 5), rep("blue", 5)),
         air = 0.01, cex = 1.25)
#
# Non-metric multidimensional scaling (axes NMDS1 vs. NMDS2) using the species (Sp-n) and 
# sites (Community-n) distances between species assemblages under two different treatments 
# accross ten sites located on the West Coast of Scotland (Stress = 0.17).
#
## 04 References ####
#
# https://jonlefcheck.net/2012/10/24/nmds-tutorial-in-r/
# https://rstudio-pubs-static.s3.amazonaws.com/246172_1930ddfb5f064b2bab54b11016ab407e.html