indices {divDyn} | R Documentation

## Scalar indices of diversity

### Description

This function includes some indices that characterize a species-abundance/occurrence distribution.

### Usage

    indices(x, samp = NULL, method = NULL)

### Arguments

`x` | either a `character` vector of occurrences or a table of counts (`matrix`).
`samp` | (`vector`): Only applicable if `x` is vector of occurrence entries. The id of the sampling units. A necessary variable for SCOR.
`method` | (`character`): The type of metric that is to be calculated. The default value (`NULL`) will calculate all implemented metrics.

### Details

This set is not complete and does not intend to supercede additional R packages (e.g. vegan). However, some metrics are presented here as they are not implemented elsewhere or because they are invoked more frequently. The following entries can be added to the `method` argument of the function, which are also named accordingly in the output table/vector.

`"richness"`: The number of sampled species.

`"shannon"`: The Shannon entropy.

`dom`: The Berger-Parker dominance index, the proportion of occurrences in the time bin that belong to the most frequent taxon.

`"hill2"`: The second order Hill number (Jost, 2006; q=2), which will be calculated by default. You can specify additional Hill numbers with adding `"hillXX"` to the `method` argument, such as `"hill3"` for (q=3). The first Hill number is defined as the exponentiad version of Shannon entropy (Eq. 3 in Jost, 2006).

`"squares"`: The 'squares' richness estimator of J. Alroy (2018).

`"chao2"`: The Chao2 estimator for incidence-based data.

`"SCOR"`: The Sum Common Species Occurrence rate of Hannisdal et al. (2012). This method will only be calculated if the occurrence entries (vector) a collection vector is provided (see examples).

### References

Alroy, J. 2018. Limits to species richness in terrestrial communities. Ecology Letters.

Hannisdal, B., Henderiks, J., & Liow, L. H. (2012). Long-term evolutionary and ecological responses of calcifying phytoplankton to changes in atmospheric CO2. Global Change Biology, 18(12), 3504–3516. https://doi.org/10.1111/gcb.12007

Jost, L. (2006). Entropy and diversity. Oikos, 113, 363–375. https://doi.org/10.1111/j.2006.0030-1299.14714.x

### Examples

    # the coral data
      data(corals)

    # Pleistocene subset
      plei <- corals[corals$stg==94,]

    # calculate everything
      pleiIndex<-indices(plei$genus, plei$coll)

[Package divDyn version 0.8.0 Index]