Principal Coordinates Analysis

Function that performs Principal Coordinates Analysis on abundance matrix.

PCO(x, dim, distfun)

# S3 method for default
PCO(x, dim = 3)

# S3 method for Dataset
PCO(x, dim = 3, distfun = dist)

Arguments

x	Distance matrix, must be a dist object, or a Dataset object. See create_dataset for more information.
dim	Number of dimensions to return.
distfun	Function that calculates distance matrix for abundance table in Dataset object.

Value

A PCO object as defined by the pco function.

Details

This is the same as function pco from the labdsv, but it includes a Dataset method.

See also

create_dataset, pca, PCA, pco, dsvdis

Examples

data(Rhizo)
data(Rhizo.map)
Dat <- create_dataset(Rhizo,Rhizo.map)

# distfun <- function(x) vegan::vegdist(x,method="bray") #requires vegan package
distfun <- dist

Dat.pco <- PCO(Dat,dim=2,distfun=distfun)
summary(Dat.pco)
#> Principal Coordinate Analysis:
#> 	 2  Components
#> 
#>   Component Var.explained Cumulative
#> 1      PCo1         41.43      41.43
#> 2      PCo2         11.81      53.24
plotgg(Dat.pco)
plotgg(Dat.pco,shape="fraction",point_size=3)
plotgg(Dat.pco,shape="fraction",col="accession",point_size=4)