[英]why it is “incorrect (no strata)” in adonis?
I am learning how to do PERMANOVA
, it is really a challenge when I started from the example. 我正在学习如何做
PERMANOVA
,当我从示例开始时,这确实是一个挑战。 The following code is from the help page in adonis
. 以下代码来自
adonis
的帮助页面。 I can go through the example, but can't figure out why it is incorrect (no strata)
? 我可以看一下示例,但无法弄清楚为什么它是
incorrect (no strata)
? Does that mean I have to obtain strata data to use adonis
? 这是否意味着我必须获取地层数据才能使用
adonis
?
data(dune)
data(dune.env)
### Example of use with strata, for nested (e.g., block) designs.
dat <- expand.grid(rep=gl(2,1), NO3=factor(c(0,10)),field=gl(3,1) )
Agropyron <- with(dat, as.numeric(field) + as.numeric(NO3)+2) +rnorm(12)/2
Schizachyrium <- with(dat, as.numeric(field)-as.numeric(NO3)+2) +rnorm(12)/2
Y <- data.frame(Agropyron, Schizachyrium)
mod <- metaMDS(Y)
plot(mod)
### Hulls show treatment
with(dat, ordihull(mod, group=NO3, show="0"))
with(dat, ordihull(mod, group=NO3, show="10", col=3))
### Spider shows fields
with(dat, ordispider(mod, group=field, lty=3, col="red"))
### Correct hypothesis test (with strata)
adonis(Y ~ NO3, data=dat, strata=dat$field, perm=999)
### Incorrect (no strata)
adonis(Y ~ NO3, data=dat, perm=999)
In PERMANOVA
, the PER
bit stands for permutation tests. 在
PERMANOVA
, PER
位代表置换测试。 Permutation tests are only valid if you shuffle samples that are truly exchangeable under the experimental design of the study. 仅当您随机整理在研究实验设计下真正可交换的样本时,置换测试才有效。 In this instance, the example uses a blocked study and hence the permutation test is only valid if you permute sample within the levels of
strata
and never between the levels of strata
. 在这种情况下,例如使用封闭的研究,因此,如果你的水平内置换样本置换检验才有效
strata
永不水平之间的strata
。
That's what the comment Incorrect (no strata)
refers to; 这就是“
Incorrect (no strata)
”注释所指的内容; that the unrestricted permutation test for these data is incorrect. 这些数据的无限制排列测试不正确。
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