distdisplayed {BiodiversityR} | R Documentation |

## Compare Distance Displayed in Ordination Diagram with Distances of Distance Matrix

### Description

This function compares the distance among sites as displayed in an ordination diagram (generated by `ordiplot`

) with the actual distances among sites as available from a distance matrix (as generated by `vegdist`

).

### Usage

```
distdisplayed(x, ordiplot, distx = "bray", plotit = T, addit = F,
method = "spearman", permutations = 100, abline = F, gam = T, ...)
```

### Arguments

`x` |
Community data frame (with sites as rows, species as columns and species abundance as cell values) or distance matrix. |

`ordiplot` |
Ordination diagram generated by |

`distx` |
Ecological distance used to calculated the distance matrix (theoretically the same distance as displayed in the ordination diagram); passed to |

`plotit` |
Should a plot comparing the distance in ordination diagram (or the distance matrix) with the distance from the distance matrix be generated (or not). |

`addit` |
Should the GAM regression result be added to an existing plot (or not). |

`method` |
Method for calculating the correlation between the ordination distance and the complete distance; from function |

`permutations` |
Number of permutations to assess the significance of the Mantel test; passed to |

`abline` |
Should a reference line (y=x) be added to the graph (or not). |

`gam` |
Evaluate the correspondence between the original distance and the distance from the ordination diagram with GAMas estimated by |

`...` |
Other arguments passed to |

### Details

This function compares the Euclidean distances (between sites) displayed in an ordination diagram with the distances of a distance matrix. Alternatively, the distances of one distance matrix are compared against the distances of another distance matrix.

These distances are compared by a Mantel test (`mantel`

) and (optionally) a GAM regression (`gam`

). Optionally, a graph is provided compairing the distances and adding GAM results.
.

### Value

The function returns the results of a Mantel test and (optionally) the results of a GAM analysis.

### 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(mgcv)
data(dune)
# pseudocount used by aitchison distance
distmatrix <- vegdist(dune, method="kulc", pseudocount=1)
ordination.model1 <- cmdscale(distmatrix,k=2)
ordiplot1 <- ordiplot(ordination.model1)
distdisplayed(dune, ordiplot=ordiplot1, distx="kulc", plotit=TRUE,
method="spearman", permutations=100, gam=TRUE)
```

*BiodiversityR*version 2.16-1 Index]