coordinates {coda.base}R Documentation

Get coordinates from compositions w.r.t. an specific basis

Description

Calculate the coordinates of a composition with respect a given basis

Usage

coordinates(
  X,
  basis = "ilr",
  label = ifelse(is.character(basis), basis, "h"),
  basis_return = TRUE
)

Arguments

X

compositional dataset. Either a matrix, a data.frame or a vector

basis

basis used to calculate the coordinates. basis can be either a string or a matrix. Accepted values for strings are: 'ilr' (default), 'clr', 'alr', 'pc', 'pb' and 'cdp'. If basis is a matrix, it is expected to have log-ratio basis given in columns.

label

name given to the coordinates

basis_return

Should the basis be returned as attribute? (default: TRUE)

Details

coordinates function calculates the coordinates of a compositiona w.r.t. a given basis. 'basis' parameter is used to set the basis, it can be either a matrix defining the log-contrasts in columns or a string defining some well-known log-contrast: 'alr' 'clr', 'ilr', 'pc', 'pb' and 'cdp', for the additive log-ratio, centered log-ratio, isometric log-ratio, clr principal components, clr principal balances or default's CoDaPack balances respectively.

Value

Coordinates of composition X with respect the given basis.

See Also

See functions ilr_basis, alr_basis, clr_basis, sbp_basis to define different compositional basis. See function composition to obtain details on how to calculate a compositions from given coordinates.

Examples

coordinates(c(1,2,3,4,5))
# basis is shown if 'coda.base.basis' option is set to TRUE
options('coda.base.basis' = TRUE)
coordinates(c(1,2,3,4,5))
# Default transformation improves performance.
N = 100
K = 1000
X = matrix(exp(rnorm(N*K)), nrow=N, ncol=K)
system.time(coordinates(X, alr_basis(K)))
system.time(coordinates(X, 'alr'))

[Package coda.base version 0.3.1 Index]