mantel_test.R

library(vegan)

## 载入需要的程辑包：permute

## 载入需要的程辑包：lattice

## This is vegan 2.5-7

data(varespec)
data(varechem)

tax.dist <- vegdist(varespec, method = "bray") # Bray-Curtis

# spec 
ph.dist <- vegdist(scale(varechem$pH), method = "euclid")
mantel(tax.dist, ph.dist, method="spear", permutations = 1000)

## 
## Mantel statistic based on Spearman's rank correlation rho 
## 
## Call:
## mantel(xdis = tax.dist, ydis = ph.dist, method = "spear", permutations = 1000) 
## 
## Mantel statistic r: 0.06857 
##       Significance: 0.20979 
## 
## Upper quantiles of permutations (null model):
##   90%   95% 97.5%   99% 
## 0.114 0.147 0.173 0.208 
## Permutation: free
## Number of permutations: 1000

#spec vs all
env.dist <- vegdist(scale(varechem), method = "euclid") # Euclidean Distance
mantel(tax.dist, env.dist, method="spear", permutations = 1000)

## 
## Mantel statistic based on Spearman's rank correlation rho 
## 
## Call:
## mantel(xdis = tax.dist, ydis = env.dist, method = "spear", permutations = 1000) 
## 
## Mantel statistic r: 0.2838 
##       Significance: 0.002997 
## 
## Upper quantiles of permutations (null model):
##   90%   95% 97.5%   99% 
## 0.121 0.158 0.176 0.211 
## Permutation: free
## Number of permutations: 1000

#

#ref https://zouhua.top/archives/d4c96916.html