R: Converting genind/genpop objects to other classes

as methods in adegenet {adegenet} | R Documentation

## Converting genind/genpop objects to other classes

### Description

These S3 and S4 methods are used to coerce genind and genpop objects to matrix-like objects. In most cases, this is equivalent to calling the `@tab` slot. An exception to this is the convertion to `ktab` objects used in the ade4 package as inputs for K-tables methods (e.g. Multiple Coinertia Analysis).

### Usage

`as(object, Class)`

### Arguments

`object`

  a genind or a genpop object.

`Class`

  the name of the class to which the object should be coerced, for instance `"data.frame"` or `"matrix"`.

### Methods

coerce

  from one object class to another using `as(object,"Class")`, where the `object` is of the old class and the returned object is of the new class `"Class"`.

### Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

### Examples

    ## Not run:
    data(microbov)
    x <- tab(microbov,NA.method="mean")
    as(x[1:3],"data.frame")

    ## dudi functions attempt to convert their first argument
    ## to a data.frame; so they can be used on genind/genpop objects.
    ## perform a PCA
    pca1 <- dudi.pca(x, scale=FALSE, scannf=FALSE)
    pca1

    x <- genind2genpop(microbov,miss="chi2")
    x <- as(x,"ktab")
    class(x)
    ## perform a STATIS analysis
    statis1 <- statis(x, scannf=FALSE)
    statis1
    plot(statis1)

    ## End(Not run)

[Package adegenet version 2.1.4 Index]