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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ordination-methods.R
\title{Perform an ordination on phyloseq data}
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ordinate(physeq, method = "DCA", distance = "bray", formula = NULL,
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\item{physeq}{(Required). Phylogenetic sequencing data
(\code{\link{phyloseq-class}}). The data on which you want to perform
the ordination. In general, these methods will be based in some fashion on
the abundance table ultimately stored as a contingency matrix 
(\code{\link{otu_table-class}}). If you're able to import data into 
\code{\link{phyloseq-class}} format, than you don't need to worry, as an
\code{otu_table} is a required component of this class. In addition, some 
ordination methods require additional data, like a constraining variable
or phylogenetic tree. If that is the case, the relevant data should be
included in \code{physeq} prior to running. Integrating the data in this way
also results in these different data components being checked for validity
and completeness by the method.}

\item{method}{(Optional). A character string. Default is \code{"DCA"}.

 Currently supported method options are:
\code{c("DCA", "CCA", "RDA", "CAP", "DPCoA", "NMDS", "MDS", "PCoA")}

    \item{DCA}{Performs detrended correspondence analysis using\code{\link{decorana}}}
    \item{CCA}{Performs correspondence analysis, 
          or optionally, constrained correspondence analysis
          (a.k.a. canonical correspondence analysis), 
          via \code{\link[vegan]{cca}}}
    \item{RDA}{Performs redundancy analysis, or optionally 
          principal components analysis, via \code{\link[vegan]{rda}}}
    \item{CAP}{[Partial] Constrained Analysis of Principal Coordinates 
          or distance-based RDA, via \code{\link[vegan]{capscale}}.
          See \code{\link[phyloseq]{capscale.phyloseq}} for more details.
          In particular, a \code{\link{formula}} argument must be provided.} 
    \item{DPCoA}{Performs Double Principle Coordinate Analysis using a 
          (corrected, if necessary) phylogenetic/patristic distance
          between species. The calculation is performed by 
          \code{\link{DPCoA}}(), which ultimately uses
          \code{\link[ade4]{dpcoa}} after making the appropriate 
          accessions/corrections of the data.}
    \item{NMDS}{Performs Non-metric MultiDimenstional Scaling of a sample-wise 
          ecological distance matrix onto a user-specified number of axes, \code{k}.
          By default, \code{k=2}, but this can be modified as a supplementary argument.
          This method is ultimately carried out by \code{\link{metaMDS}} after the 
          appropriate accessions and distance calculations.
          Because \code{metaMDS} includes its own distance 
          calculation wrappers to \code{\link[vegan]{vegdist}}, and these provide
          additional functionality in the form of species scores,
          \code{ordinate} will pass-on the \code{distance} 
          argument to \code{metaMDS} if it is among the 
          supported \code{vegdist} methods. However, all distance methods
          supported by \code{\link{distance}} are supported here,
          including \code{"unifrac"} (the default) and \code{"DPCoA"}.}
    \item{MDS/PCoA}{Performs principal coordinate analysis 
          (also called principle coordinate decomposition, 
          multidimensional scaling (MDS), or classical scaling)
          of a distance matrix (Gower 1966), 
          including two correction methods for negative eigenvalues.
          \code{\link[ape]{pcoa}} for further details.

\item{distance}{(Optional). A character string. Default is \code{"bray"}.
 The name of a supported \code{\link{distance}} method; 
 or, alternatively, 
 a pre-computed \code{\link{dist}}-class object.
 This argument is only utilized
 if a distance matrix is required by the ordination method specified by the
 \code{method} argument (above).

 Any supported \code{\link{distance}} methods 
 are supported arguments to \code{distance} here. 
 See \code{\link{distance}} for more details, examples.}

\item{formula}{(Optional). A model \code{\link{formula}}.
Only relevant for certain ordination methods.
The left hand side is ignored, defined by 
the \code{physeq} and \code{distance} arguemnts.
The right hand side gives the constraining variables,
and conditioning variables can be given 
within a special function \code{Condition}.
See \code{\link[vegan]{cca}} or \code{\link[vegan]{capscale}}
for examples/details.}

\item{...}{(Optional). Additional arguments to supporting functions. For 
example, the additional argument \code{weighted=TRUE} would be passed on
to \code{\link{UniFrac}} if \code{"unifrac"} were chosen as the
\code{distance} option and \code{"MDS"} as the ordination \code{method}
option. Alternatively, if \code{"DCA"} were chosen as the 
ordination \code{method} option, additional arguments would be passed on
to the relevant ordination function, \code{\link{decorana}}, for example.}
An ordination object. The specific class of the returned object depends upon the 
 ordination method, as well as the function/package that is called internally
 to perform it.
 As a general rule, any of the ordination classes
 returned by this function will be recognized by downstream tools in the
 \code{phyloseq} package, for example the ordination plotting 
 function, \code{\link{plot_ordination}}.
This function wraps several commonly-used ordination methods. The type of 
ordination depends upon the argument to \code{method}. Try 
\code{ordinate("help")} or \code{ordinate("list")} for the currently
supported method options.
# See http://joey711.github.io/phyloseq/plot_ordination-examples
# for many more examples.
# plot_ordination(GP, ordinate(GP, "DCA"), "samples", color="SampleType")
\href{http://joey711.github.io/phyloseq/plot_ordination-examples}{The plot_ordination Tutorial}

 Related component ordination functions described within phyloseq:


 Described/provided by other packages:

 \code{\link{cca}}/\code{\link{rda}}, \code{\link{decorana}}, \code{\link{metaMDS}}, 
 \code{\link{pcoa}}, \code{\link[vegan]{capscale}}

 NMDS and MDS/PCoA both operate on distance matrices, typically based on some
 pairwise comparison of the microbiomes in an experiment/project. There are
 a number of common methods to use to calculate these pairwise distances, and
 the most convenient function (from a \code{phyloseq} point of view) for calculating 
 these distance matrices is the 


 function. It can be 
 thought of as a distance / dissimilarity-index companion function for
 \code{ordinate}, and indeed the distance options provided to \code{ordinate}
 are often simply passed on to \code{\link{distance}}.

 A good quick summary of ordination is provided in the introductory vignette
 for vegan:

 \href{http://cran.r-project.org/web/packages/vegan/vignettes/intro-vegan.pdf}{vegan introductory vignette}

 The following \code{R} task views are also useful for understanding the 
 available tools in \code{R}:

\href{http://cran.r-project.org/web/views/Environmetrics.html}{Analysis of Ecological and Environmental Data}

\href{http://cran.r-project.org/web/views/Multivariate.html}{Multivariate Statistics}