Description Usage Arguments Details Value Examples

This function makes pairwise/ setwise combinations of sites in the community matrix x and calculates pairwise/ setwise beta diversities, respectively. "Set" refers to a user-defined number of samples that will be used. This is essentially the number of plots in a sample-based rarefaction. It's default is 2 (i.e. pairs).

1 2 3 4 5 6 7 8 9 10 | ```
beta_stand(
x,
setsize = 2,
func = list("beta_true"),
args = NULL,
summarise = T,
max_combn = 10000,
resamples = 1000,
verbose = T
)
``` |

`x` |
A site by species matrix. |

`setsize` |
Number of samples per subset. |

`func` |
a list of function names to be used for the metric calculation |

`args` |
a list of additional arguments to be passed on to the functions in func |

`summarise` |
Return mean and variance of all betas? |

`max_combn` |
Number of combinations allowed before resampling is used instead |

`resamples` |
Number of samples used if possible combinations exceeds max_combn |

`verbose` |
Print notifications? |

The calulation of the beta-diversity metric is done according to the function in "func". This should be a function that returns a (dis-)similarity or beta diversity metric for a site-by species matrix like x. "func" is applied to every subset. Addidtional arguments will be passed on to "func".

If the number of possible sets/ pairwise comparisons exceeds the value of max_combn. A random subsample of all combinations will be drawn. The number of random samples can be adjusted using the argument resamples. It is not recommended increase the value of max_combn. The function choose() "n over k" can be used to manually compute the number of possible subsets where n is the number of samples/rows in x and k is setsize. If summarise = T, mean and variance of all setwise comparisons are returned. Otherwise, the function returns all individual beta values.

A data frame

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