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vegan - NMDS 为 ANOSIM 和 ADONIS 提供了相互矛盾的结果

问题描述

我正在测试捕捞区和禁捕区之间群落组成的差异，虽然 nmds 似乎表明两个级别有很大重叠，但 ANOSIM 和 ADONIS 表明存在显着差异。我是否做错了什么，或者我看不到这种显着差异的原因？

species

env=species[,1]
species=species[,-1]
species = species[,colSums(species) > 2]

nmds=metaMDS(species, distance="bray", k=3, type="n", trymax=100)
nmds
env$Protection=as.factor(env$Protection)
pointvec <- c(21, 21)
bgvec <- c("black","white")
with(env, levels(Protection))
plot(nmds,type="n",xaxt='n',xlab="",cex.lab=1.5,cex.axis=1.4,xlim=c(-1.5,1.5),ylim=c(-1.2,1))
axis(side=1)
with(env, points(nmds,pch=pointvec[Protection],cex=1,bg = bgvec[Protection],type="p" ,display="sites"))
ordiellipse(nmds, groups=env$Protection, kind = "se", conf = 0.95)
legend("topleft", "A", bty="n",cex=1.5,inset=-0.02,adj=1) 
legend("bottomright", "Stress = 0.182", bty="n",cex=1.5) 
with(env,legend("topright", legend =  levels(Protection),inset=-0.007,cex=1.5,bty="n",pt.bg =    bgvec,pch=pointvec))

nmds 图显示组的紧密重叠

spe.dist <- vegdist(species,method='bray')
spe.ano <- anosim(spe.dist, env$Protection)
summary(spe.ano)

#Call:
#anosim(x = spe.dist, grouping = env$Protection) 
#Dissimilarity: bray 

#ANOSIM statistic R: 0.04693 
      #Significance: 0.029 

#Permutation: free
#Number of permutations: 999

#Upper quantiles of permutations (null model):
   #90%    95%  97.5%    99% 
#0.0290 0.0398 0.0487 0.0593 

#Dissimilarity ranks between and within classes:
       # 0%     25%     50%     75% 100%    N
#Between  1 655.625 1193.50 1771.25 2317 1184
#fished   3 750.500 1360.00 1896.50 2317  666
 #no-take  2 358.125  837.25 1525.00 2285  496

然后 permanova 给出了类似的结果

adonis(species~env$Protection,method='bray')

#Call:
#adonis(formula = species ~ env$Protection, method = "bray") 
#Permutation: free
#Number of permutations: 999
#Terms added sequentially (first to last)

              # Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)   
#env$Protection  1    0.9517 0.95174  2.8946 0.04141  0.002 **
#Residuals      67   22.0296 0.32880         0.95859          
#Total          68   22.9813                 1.00000          
 #---
#Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

标签： vegan

解决方案

首先，NMDS 图形和您的测试不一致：测试是针对类质心的位置，但图表显示了观察的分布。ordiellipse(..., kind = "se", conf = 0.95)会更符合测试。其次，测试（特别是adonis- 我不会使用anosim）基于解释为欧几里得的完整n维空间，而 NMDS 是非欧几里得差异的二维映射（尽管 NMDS 图本身是欧几里得）。可能是您的组在您未估计的第三维度上有所不同。

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