英文:
PERMANOVA - unbalanced design
问题
我是新手，对统计分析和R不太熟悉。我有8个池塘中5个分类群的相对丰度数据（以百分比表示）。这8个池塘中的样本数量在7到12之间（使设计不平衡）。我可以使用PERMANOVA（vegan::adonis2）和PERMDISP来测试这5个分类群在8个池塘中的组成是否不同吗？
谢谢！
我已经尝试了以下方法：
matrix<-as.matrix(Data[,c(5:9)]) # 列5到9是指相对丰度百分比的5个分类群
dist<-vegdist(matrix, method="robust.aitchison", na.rm = F)
adonis2(dist~ Pond, data=Data)
anova(betadisper(dist,Data$Pond))
这个结果是否意味着池塘之间没有差异？我如何分析池塘之间各个分类群的差异呢？
谢谢！
英文:
I am new to statistical analysis and R. I have data of relative abundance (in percentage) of 5 taxa in 8 ponds. The number of samples in the 8 ponds ranges from 7 to 12 (making the design unbalanced). Can I use PERMANOVA (vegan::adonis2) and PERMDISP to test if the composition of the 5 taxa is different in the 8 ponds?
Thank you!
I have tried as follows:
matrix<-as.matrix(Data[,c(5:9)]) # columns 5:9 refers to relative abundance of the 5 taxa in percentage
dist<-vegdist(matrix, method="robust.aitchison", na.rm = F)
adonis2(dist~ Pond, data=Data)
anova(betadisper(dist,Data$Pond))
Does the result mean that there are no difference between the ponds as a whole? And how can I analyse the differences of individual taxon among the ponds?
Thank you!
答案1
得分: 0
Yeah, that's fine. But you don't want the anova() method for betadisper() objects; you should use permutest() on the betadisper() object to get the permutation test of heterogeneous dispersions.
The results of the PERMANOVA mean you fail to reject the null hypothesis that the variation explained by Pond is consistent with the Null hypothesis of no effect. The results do not indicate there is no difference between ponds; there are differences (otherwise the SumOfSqs would be 0), but they are just small.
Analysing the per taxon differences would just be a univariate model so not really something you would do with adonis2()...
英文:
Yeah, that's fine. But you don't want the anova() method for betadisper() objects; you should use permutest() on the betadisper() object to get the permutation test of heterogeneous dispersions.
The results of the PERMANOVA mean you fail to reject the null hypothesis that the variation explained by Pond is consistent with the Null hypothesis of no effect. The results do not indicate there is no difference between ponds; there are differences (otherwise the SumOfSqs would be 0), but they are just small.
Analysing the per taxon differences would just be a univariate model so not really something you would do with adonis2()...
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