cca.phyloseq {phyloseq} | R Documentation

## Constrained Correspondence Analysis and Redundancy Analysis.

### Description

This is the internal function that simplifies getting phyloseq data into the constrained ordination functions, `cca` and `rda`. Unlike `capscale.phyloseq`, the formula argument to these methods is optional, and results in an unconstrained ordination.

### Usage

    cca.phyloseq(physeq, formula = NULL, method = "CCA", ...)

    ## S4 method for signature 'phyloseq,formula'
    cca.phyloseq(physeq, formula = NULL,
      method = "CCA", ...)

    ## S4 method for signature 'otu_table,ANY'
    cca.phyloseq(physeq, formula = NULL,
      method = "CCA", ...)

    ## S4 method for signature 'phyloseq,'NULL''
    cca.phyloseq(physeq, formula = NULL,
      method = "CCA", ...)

### Arguments

`physeq` | (Required). Phylogenetic sequencing data (`phyloseq-class`). The data on which you want to perform the ordination.
`formula` | (Optional). A `formula`, specifying the contraining variable(s) format, with variable names corresponding to `sample_data` (RHS) from within `physeq`.
`method` | (Optional). A single `character` string, specifying `"RDA"` or `"CCA"`. Default is `"CCA"`.
`...` | (Optional). Additional named arguments passed to `capscale`.

### Value

same output as `cca` or `rda`, respectively.

### See Also

`plot_ordination`, `rda`, `cca`

### Examples

    #
    # cca.phyloseq(physeq, formula, method, ...)

[Package phyloseq version 1.38.0 Index]