Description Usage Arguments Value References See Also Examples

Computes the distance decay of zeta diversity for a range of orders (number of assemblages or sites), using generalised linear models.

1 2 3 4 5 |

`xy` |
Site-by-coordinate data frame, with sites as rows and coordinates as columns. |

`data.spec` |
Site-by-species presence-absence data frame, with sites as rows and species as columns. |

`orders` |
Range of number of assemblages or sites at which zeta diversity is computed. All the orders must be striclty greater than 1. |

`sam` |
Number of samples for which the zeta diversity is computed. |

`family` |
A description of the error distribution and link function to be used in the generalised linear models (see |

`distance.type` |
Method to compute distance. Default is " |

`dist.custom` |
Distance matrix provided by the user when |

`method` |
Name of a function (as a string) indicating how to combine the pairwise differences and distances for more than 3 sites. It can be a basic R-function such as " |

`confint.level` |
Percentage for the confidence intervals of the coefficients from the linear regression. |

`trsf` |
Name of a function (as a string) indicating how to transform distance. Default is "NULL" for the identity transformation. |

`cutoff` |
If specified, maximum distance value for which the linear regression must be performed. |

`rescale` |
Boolean value (TRUE or FALSE) indicating if the zeta values should be divided by |

`normalize` |
Boolean value (TRUE or FALSE) indicating if the zeta values for each sample should be divided by the total number of species for this specific sample. |

`plot` |
Boolean value (TRUE or FALSE) indicating if the outputs must be plotted. |

`Zeta.ddecays`

returns a list containing the following components:

`orders` |
Range of number of assemblages or sites at which zeta diversity was computed. |

`coefs` |
A vector of the coefficients from the generalised linear models for the numbers of sites specified by |

`confint` |
The confidence intervals for the coefficients from the generalised linear models. |

Hui C. & McGeoch M.A. (2014). Zeta diversity as a concept and metric that unifies incidence-based biodiversity patterns. *The American Naturalist*, 184, 684-694.

`Zeta.decline.mc`

, `Zeta.order.mc`

, `Zeta.decline.ex`

, `Zeta.order.ex`

, `Zeta.ddecay`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
utils::data(bird.spec.coarse)
xy.bird <- bird.spec.coarse[,1:2]
data.spec.bird <- bird.spec.coarse[,3:193]
dev.new()
zeta.ddecays.bird <- Zeta.ddecays(xy.bird, data.spec.bird, sam = 100, orders = 2:5,
plot = TRUE, confint.level = 0.95)
##########
utils::data(Marion.species)
xy.marion <- Marion.species[,1:2]
data.spec.marion <- Marion.species[,3:33]
dev.new()
zeta.ddecays.marion <- Zeta.ddecays(xy.marion, data.spec.marion, sam = 100,
orders = 2:5, plot = TRUE, confint.level = 0.95)
``` |

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.