Coordinates of compositions with respect to a basis

Compute coordinates of a composition or a compositional data set with respect to a given log-ratio basis.

The `basis` argument can be either:

• a character string identifying a predefined coordinate system, or

• a matrix whose columns define a system of log-contrasts.

The predefined options are:

• `"ilr"`: isometric log-ratio coordinates,

• `"olr"`: orthonormal log-ratio coordinates,

• `"clr"`: centered log-ratio coordinates,

• `"alr"`: additive log-ratio coordinates,

• `"pw"`: pairwise log-ratios,

• `"pc"`: principal component log-ratio coordinates,

• `"pb"`: principal balance coordinates,

• `"cdp"`: CoDaPack default balances.

coordinates(X, basis = "ilr")

coord(..., basis = "ilr")

alr_c(X)

clr_c(X)

ilr_c(X)

olr_c(X)

Arguments

X

A compositional data set. It can be a numeric matrix, a data frame, or a numeric vector.

basis

Basis used to compute the coordinates. Either a character string naming a predefined basis or a matrix with log-ratio basis vectors in columns.

...

components of the composition

Value

Coordinates of `X` with respect to the given `basis`. The returned object has the same general type as the input when possible.

See also

ilr_basis, alr_basis, clr_basis, sbp_basis, composition

Examples

coordinates(1:5)
#>       ilr1       ilr2       ilr3       ilr4 
#> -0.4901291 -0.6140370 -0.6833297 -0.7288906 

B <- ilr_basis(5)
coordinates(1:5, B)
#>       ilr1       ilr2       ilr3       ilr4 
#> -0.4901291 -0.6140370 -0.6833297 -0.7288906 

X <- rbind(1:5, 2:6)
coordinates(X, "clr")
#>            clr1       clr2       clr3      clr4      clr5
#> [1,] -0.9574983 -0.2643512 0.14111394 0.4287960 0.6519396
#> [2,] -0.6227031 -0.2172380 0.07044412 0.2935877 0.4759092