# 【5.4.2】PERMANOVA分析--解析处理对微生物群落的作用大小

Fig. 3. PERMANOVA values showing the percent that fertilization and aggregate fractions contributed to the variation in bacterial (a) and fungal (b) community compositions.

## 一、数据分析

PERMANOVA分析 （数据可后台获取）

otu<-read.csv("D://test_otu.csv",row.names = 1)
design<-read.csv("D://test_design.csv")
library(vegan)

results<- adonis(formula = t(otu[,1:64]) ~ (design$Group * design$Treatment),data = design, permutations = 999, method = "bray")


Call:

adonis(formula = t(otu[, 1:64]) ~ (design$Group * design$Treatment),      data = design, permutations = 999, method = "bray")

Permutation: free

Number of permutations: 999

Terms added sequentially (first to last)

Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)

design$Group 1 6.8904 6.8904 52.207 0.42772 0.001 *** design$Treatment  2    1.3002  0.6501   4.926 0.08071  0.001 ***

Residuals        60    7.9189  0.1320         0.49157

Total            63   16.1095                 1.00000

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Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1


## 二、计算原理

PERMANOVA是生态学分析中常用的统计方法，可以计算不同环境因子与群落组成之间是否存在相关性。PERMANOVA由McArdle和Anderson于2001年提出。

PERMANOVA利用对样本进行随机置换的方式，生成一个F值的分布，然后求得P值。