as_composition {nexus} | R Documentation |
Coerce to a Closed Compositional Matrix
Description
Coerces an object to a CompositionMatrix
object.
Usage
as_composition(from, ...)
## S4 method for signature 'numeric'
as_composition(from)
## S4 method for signature 'matrix'
as_composition(from)
## S4 method for signature 'data.frame'
as_composition(
from,
codes = NULL,
samples = NULL,
groups = NULL,
auto = getOption("nexus.autodetect"),
verbose = getOption("nexus.verbose")
)
Arguments
from |
A |
... |
Currently not used. |
codes |
An |
samples |
An |
groups |
An |
auto |
A |
verbose |
A |
Details
The CompositionMatrix
class has special slots:
-
codes
for laboratory codes, -
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.
See vignette("nexus")
.
Value
A CompositionMatrix
object.
Note
All non-numeric variable will be removed.
Author(s)
N. Frerebeau
See Also
Other compositional data tools:
as_amounts()
,
as_features()
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
get_totals(B)
## This allows to restore the source data
A2 <- as_amounts(B)
## Coerce to a data.frame
X <- data.frame(B)
head(X)