estimate_richness {phyloseq} | R Documentation

## Summarize alpha diversity

### Description

Performs a number of standard alpha diversity estimates, and returns the results as a `data.frame`. Strictly speaking, this function is not only estimating richness, despite its name. It can operate on the cumulative population of all samples in the dataset, or by repeating the richness estimates for each sample individually. NOTE: You must use untrimmed datasets for meaningful results, as these estimates (and even the “observed” richness) are highly dependent on the number of singletons. You can always trim the data later on if needed, just not before using this function.

### Usage

    estimate_richness(physeq, split = TRUE, measures = NULL)

### Arguments

`physeq` | (Required). `phyloseq-class`, or alternatively, an `otu_table-class`. The data about which you want to estimate the richness.
`split` | (Optional). Logical. Should a separate set of richness estimates be performed for each sample? Or alternatively, pool all samples and estimate richness of the entire set.
`measures` | (Optional). Default is `NULL`, meaning that all available alpha-diversity measures will be included. Alternatively, you can specify one or more measures as a character vector of measure names. Values must be among those supported: `c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher")`.

### Value

A `data.frame` of the richness estimates, and their standard error.

### See Also

Check out the custom plotting function, `plot_richness`, for easily showing the results of different estimates, with method-specific error-bars. Also check out the internal functions borrowed from the `vegan` package:

`estimateR`

`diversity`

`fisherfit`

### Examples

    ## There are many more interesting examples at the phyloseq online tutorials.
    ## http://joey711.github.com/phyloseq/plot_richness-examples
     data("esophagus")
     # Default is all available measures
     estimate_richness(esophagus)
     # Specify just one:
     estimate_richness(esophagus, measures="Observed")
     # Specify a few:
     estimate_richness(esophagus, measures=c("Observed", "InvSimpson", "Shannon", "Chao1"))

[Package phyloseq version 1.34.0 Index]