subset.procmod_frame {ProcMod}

Subsetting Procmod Frames

Description

This is the implementation of the subset generic function for procmod_frame.

Usage

## S3 method for class 'procmod_frame'
subset(x, subset, select, drop = FALSE, ...)

Arguments

x

object to be subsetted.

subset

logical expression indicating elements or rows to keep: missing values are taken as false.

select

expression, indicating columns to select from a data frame.

drop

passed on to [ indexing operator.

...

further arguments to be passed to or from other methods.

Details

The subset argument works on rows. Note that subset will be evaluated in the procmod_frame, so columns can be referred to (by name) as variables in the expression (see the examples).

The select argument if provided indicates with matrices have to be conserved. It works by first replacing column names in the selection expression with the corresponding column numbers in the procmod_frame and then using the resulting integer vector to index the columns. This allows the use of the standard indexing conventions so that for example ranges of columns can be specified easily, or single columns can be dropped (see the examples). Remember that each column of a procmod_frame is actually a matrix.

The drop argument is passed on to the procmod_frame indexing method. The default value is FALSE.

Value

A procmod_frame containing just the selected rows and columns.

Author(s)

Eric Coissac

Christelle Gonindard-Melodelima

Examples

library(vegan)
data(bacteria)
data(eukaryotes)
data(soil)

dataset <- procmod_frame(euk = vegdist(decostand(eukaryotes,
                                                 method = "hellinger"),
                                       method = "euclidean"),
                         bac = vegdist(decostand(bacteria,
                                                 method = "hellinger"),
                                       method = "euclidean"),
                         soil = scale(soil,
                                      center = TRUE,
                                      scale  = TRUE))
dim(dataset)

higher_ph = subset(dataset,soil[,"pH"] > 0)
dim(higher_ph)

without_bacteria = subset(dataset,soil[,"pH"] > 0, -bac)
dim(without_bacteria)