mantelTest {biotools} | R Documentation |

## Mantel's Permutation Test

### Description

Mantel's permutation test based on Pearson's correlation coefficient to evaluate the association between two distance square matrices.

### Usage

```
mantelTest(m1, m2, nperm = 999, alternative = "greater",
graph = TRUE, main = "Mantel's test", xlab = "Correlation", ...)
```

### Arguments

`m1` |
an object of class "matrix" or "dist", containing distances among |

`m2` |
an object of class "matrix" or "dist", containing distances among |

`nperm` |
the number of matrix permutations. |

`alternative` |
a character specifying the alternative hypothesis. It must be one of "greater" (default), "two.sided" or "less". |

`graph` |
logical; if TRUE (default), the empirical distribution is plotted. |

`main` |
opitional; a character describing the title of the graphic. |

`xlab` |
opitional; a character describing the |

`...` |
further graphical arguments. See |

### Value

A list of

`correlation` |
numeric; the observed Pearson's correlation between |

`p.value` |
numeric; the empirical p-value of the permutation test. |

`alternative` |
character; the alternative hypothesis used to compute |

`nullcor` |
numeric vector containing randomized values of correlation, i.e., under the null hypothesis that the true correlation is equal to zero. |

### Author(s)

Anderson Rodrigo da Silva <anderson.agro@hotmail.com>

### References

Mantel, N. (1967). The detection of disease clustering and a generalized regression approach.
*Cancer Research*, 27:209–220.

### See Also

### Examples

```
# Distances between garlic cultivars
data(garlicdist)
garlicdist
# Tocher's clustering
garlic <- tocher(garlicdist)
garlic
# Cophenetic distances
coph <- cophenetic(garlic)
coph
# Mantel's test
mantelTest(garlicdist, coph,
xlim = c(-1, 1))
# End (Not run)
```

*biotools*version 4.2 Index]