RAM (version 1.2.0)

assist.ordination: Perform CCA and RDA Analysis for OTU Tables

Description

This function simplifies CCA and RDA analysis by abstracting away some of the complexity and returning a list of useful measures.

Usage

assist.cca(otu1, otu2 = NULL, meta, full = TRUE, exclude = NULL, 
           rank, na.action=na.exclude)
assist.rda(otu1, otu2 = NULL, meta, full = TRUE, exclude = NULL, 
           rank, na.action=na.exclude)

Arguments

otu1

the first OTU table to be used.

otu2

the second OTU table to be used.

meta

the metadata table to be used (must have same samples as otu1/otu2).

full

logical. Should a full model be considered? (If not, a restricted model is used).

exclude

A vector, either numeric or logical, specifying the columns to be removed from meta. If a character vector, columns with those names will be removed; if a numeric vector, columns with those indices will be removed.

rank

a character vector representing a rank. Must be in one of three specific formats (see ?RAM.rank.formatting for help).

na.action

choice of one of the following: "na.fail", "na.omit" or "na.exclude", see na.action in cca for detail.

Value

• If both otu1 and otu2 are given, a list of length 2 will be returned with the following items (if only otu1 is given, a list of length 1 will be returned with these items):
• $GOF
  the goodness of fit scores for the model.
• $VIF
  the VIF scores for the model.
• $percent_variation
  the percent variation explained by each axis
• $CCA_eig
  Eigenvalues for CCA axes.
• $CA_eig
  Eigenvalues for CA axes.
• $anova
  the ANOVA results for the model.

See Also

cca, anova.cca

Examples

data(ITS1, meta)

cca.help <- assist.cca(ITS1, meta=meta, rank="p")
cca.help$anova