Mantel_tests.Rmd

---
title: "Mantel tests"
output: html_notebook
---

This is an Mantel tests Rmd file, introduce how to analysis Mantel tests.


```{r}
library(tidyverse)
library(vegan)
```

Add a new chunk by clicking the *Insert Chunk* button on the toolbar or by pressing *Cmd+Option+I*.

When you save the notebook, an HTML file containing the code and output will be saved alongside it (click the *Preview* button or press *Cmd+Shift+K* to preview the HTML file). 

The preview shows you a rendered HTML copy of the contents of the editor. Consequently, unlike *Knit*, *Preview* does not run any R code chunks. Instead, the output of the chunk when it was last run in the editor is displayed.

```{r}
otu.dist <- vegdist(otu, method = 'bray')
env.scale <- scale(env, center = TRUE, scale = TRUE)
env.dist <- dist(env.scale, method = 'euclidean')

```

**重点**

对于env环境数据，根据其尺度的具体情况一般是需要进行scale
```{r}
mantel.result <- mantel(otu.dist, env.dist, method = 'spearman', permutations = 9999, na.rm = TRUE)

```