Coerce to a Closed Compositional Matrix

Coerces an object to a CompositionMatrix object.

Usage

as_composition(from, ...)

# S4 method for matrix
as_composition(from)

# S4 method for data.frame
as_composition(from, samples = NULL, groups = NULL)

Arguments

from

A matrix or data.frame to be coerced.

...

Currently not used.

samples

An integer giving the index of the column to be used for sample identification: allows to identify replicated measurements. If NULL (the default), row names will be used as sample IDs.

groups

An integer giving the index of the column to be used to group the samples. If NULL (the default), no grouping is stored.

Value

A CompositionMatrix object.

Details

The CompositionMatrix class has special slots (see vignette("manual")):

• samples for repeated measurements/observation,

• groups to group data by site/area.

When coercing a data.frame to a CompositionMatrix object, an attempt is made to automatically assign values to these slots by mapping column names (case insensitive, plural insensitive). This behavior can be disabled by setting options(nexus.autodetect = FALSE) or overridden by explicitly specifying the columns to be used.

Note

All non-numeric variable will be removed.

See also

Other compositional data tools: as_amounts(), closure()

Author

N. Frerebeau

Examples

## Create a count matrix
A1 <- matrix(data = as.numeric(sample(1:100, 100, TRUE)), nrow = 20)

## Coerce to compositions
B <- as_composition(A1)

## Row sums are internally stored before coercing to relative frequencies
## (use get_totals() to retrieve these values)
## This allows to restore the source data
A2 <- as_amounts(B)

## Coerce to an S3 data.frame
X <- data.frame(B)
head(X)
#>            col1      col2      col3       col4       col5 samples
#> row1 0.06250000 0.2416667 0.3000000 0.33750000 0.05833333    row1
#> row2 0.19217082 0.1530249 0.2526690 0.12811388 0.27402135    row2
#> row3 0.28630705 0.1203320 0.3734440 0.02489627 0.19502075    row3
#> row4 0.25885559 0.1771117 0.1035422 0.19618529 0.26430518    row4
#> row5 0.05666667 0.2033333 0.2400000 0.16666667 0.33333333    row5
#> row6 0.27483444 0.1788079 0.2880795 0.22847682 0.02980132    row6