#####################################
#Load libraries
#####################################
library(BiodiversityR)
library(labdsv)

#####################################
#Load Data
#####################################
one_year<-read.csv("burn1.csv",header=TRUE,row.names="year")
twenty_year<-read.csv("burn20.csv",header=TRUE,row.names="year")
time<-read.csv("time.csv",header=TRUE,row.names="year")

one_year_log <- disttransform(one_year, method='log')
twenty_year_log <- disttransform(twenty_year, method='log')

#####################################
#MANTEL test using quantitative similarity and pearson correlation
#####################################
community_distance<-vegdist(one_year_log, method='bray')
time_distance<-vegdist(time, method='euclidean')
mantel<-mantel(time_distance, community_distance, method="pearson", permutations=1000)
plot(time_distance, community_distance)
mantel
hist(mantel$perm)

#same analysis with the 20 year burn regime
community_distance<-vegdist(twenty_year_log, method='bray')
time_distance<-vegdist(time, method='euclidean')
mantel<-mantel(time_distance, community_distance, method="pearson", permutations=1000)
plot(time_distance, community_distance)
mantel
hist(mantel$perm)

#####################################
#MANTEL test using qualitative similarity and spearman rank correlation
#####################################
community_distance<-dsvdis(one_year, index="steinhaus")
time_distance<-vegdist(time, method='euclidean')
mantel<-mantel(time_distance, community_distance, method="spearman", permutations=1000)
plot(time_distance, community_distance)
mantel
hist(mantel$perm)