#[NMDS using foraging data; R] Fig. 4(b)

library(vegan) 
library(ecodist) 
library(ggplot2)

# Import the foraging data
name = read.csv("hirakawa_data.csv",header=TRUE,row.names=1)
s_name<-name[,3:7]
m_name = as.matrix(s_name)
set.seed(123)

#NMDS
nmds = metaMDS(m_name, distance = "bray")
data.scores = as.data.frame(scores(nmds)$sites)
data.scores$lineage = name$lineage

#Visualization
ggplot(data.scores,aes(x=NMDS1, y=NMDS2, color=`lineage`, shape=`lineage`)) +
  geom_point(size = 5) + 
  scale_shape_manual(values=c(16,17,18), name="lineage") + 
  scale_colour_manual(values = c("rosybrown1", "cadetblue1", "royalblue")) +
  xlab(paste("NMDS1")) +
  ylab(paste("NMDS2")) +
  ggtitle("NMDS")+
  theme_bw() + 
  theme(
    text = element_text(size = 13),
    axis.title.x  = element_text(size = 13), 
    axis.title.y  = element_text(size = 13), 
    legend.text = element_text(size= 10)) +
  theme(aspect.ratio=1, plot.title=element_text(size=12, face="bold"))

# PERMANOVA
adonis2(m_name ~ lineage+sex, method="bray")