# similarity: Similarity Summary Table In vegetarian: Jost Diversity Measures for Community Data

## Description

Creates a summary table of community overlap for all possible pairwise combinations of samples (e.g. sites, plots) using the `similarity` function.

## Usage

 `1` ```similarity(abundances, abundances2 = NULL, q = 1, boot = FALSE, boot.arg = list(s.sizes = NULL, num.iter = 100)) ```

## Arguments

 `abundances` Community data as a matrix where columns are individual species and rows are sites. Matrix elements are abundance data (e.g. counts, percent cover estimates). May be given as a vector with abundances2 as a vector for a second community. `abundances2` Community data, a vector of different species within a site. Vector elements are abundance data (e.g. counts, percent cover estimates). If abundances is given a matrix, then abundances2 defaults to a logical FALSE statement. `q` Order of the diversity measure. Defaults to the Shannon case where q = 1. `boot` Logical indicating whether to use bootstrapping to estimate uncertainty. `boot.arg` (optional) List of arguments to pass bootstrapping function: list(s.sizes=number you specify, num.iter=number you specify)

## Details

This function calculates pairwise similarity for two or more samples, so the abundance data must be a matrix with two or more rows (samples). Depending on the specification of the order (q), other different similarity indices may be calculated (e.g. Sorenson index when q=0, Horn index when q=1, Morisita-Horn index when q=2) (Jost 2007).

## Value

 `Similarity` A matrix of pairwise similarities showing community overlap calculated using the similarity function. `StdErr` (optional) Standard error of value estimated through bootstrapping.

## Author(s)

Noah Charney, Sydne Record

## References

Jost, L. 2007. Partitioning diversity into independent alpha and beta components. Ecology 88(10): 2427-2439.

`sim.table`, `sim.groups`, `bootstrap`

## Examples

 ```1 2 3 4 5 6 7``` ```data(simesants) hemlock<-subset(simesants,Habitat=="Hemlock")[,-1] hardwood<-subset(simesants,Habitat=="Hardwood")[,-1] similarity(rbind(hemlock,hardwood)) similarity(hemlock,abundances2=hardwood) similarity(hemlock,abundances2=hardwood,boot=TRUE) similarity(hemlock,abundances2=hardwood,q=2,boot=TRUE,boot.arg=list(num.iter=200)) ```

### Example output

```[1] 0.8847291
[1] 0.8847291
\$Simlarity
[1] 0.8847291

\$StdErr
[1] 0.02305693

\$Simlarity
[1] 0.9478082

\$StdErr
[1] 0.01632159
```

vegetarian documentation built on May 29, 2017, 10:48 a.m.