NMSrandom {BiodiversityR} | R Documentation |

## Calculate the NMS Result with the Smallest Stress from Various Random Starts

### Description

This function provides a simplified version of the method of calculating NMS results implemented by the function `metaMDS`

(vegan).

### Usage

```
NMSrandom(x,perm=100,k=2,stressresult=F,method="isoMDS")
```

### Arguments

`x` |
Distance matrix. |

`perm` |
Number of permutations to select the configuration with the lowest stress. |

`k` |
Number of dimensions for the non metric scaling result; passed to |

`stressresult` |
Provide the calculated stress for each permutation. |

`method` |

### Details

This function is an easier method of calculating the best NMS configuration after various random starts than implemented in the `metaMDS`

function (vegan). The function uses a distance matrix (as calculated for example by function `vegdist`

from a community data set) and calculates random starting positions by function `initMDS`

(vegan) analogous to `metaMDS`

.

### Value

The function returns the NMS ordination result with the lowest stress (calculated by `isoMDS`

or `sammon`

.), or the stress of each NMS ordination.

### Author(s)

Roeland Kindt (World Agroforestry Centre)

### References

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.

https://www.worldagroforestry.org/output/tree-diversity-analysis

### Examples

```
library(vegan)
library(MASS)
data(dune)
distmatrix <- vegdist(dune)
Ordination.model1 <- NMSrandom(distmatrix, perm=100, k=2)
Ordination.model1 <- add.spec.scores(Ordination.model1, dune,
method='wa.scores')
Ordination.model1
```

*BiodiversityR*version 2.16-1 Index]