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coda.base

Compositional Bases for Log-Ratio Transformations

This R package provides tools for working with compositional data using log-ratio methodology, following the foundational work of Aitchison and further developments by Egozcue and collaborators.

The package is focused on the construction and use of orthonormal and non-orthonormal bases for the representation of compositions in real coordinates, enabling advanced statistical modeling and interpretation.

Key Functions

• ilr_basis(), alr_basis(), clr_basis() – classical log-ratio bases:

  • ILR/OLR (Isometric/Orthonormal Log-Ratio): orthonormal basis.
  • ALR (Additive Log-Ratio): basis with respect to a reference part.
  • CLR (Centered Log-Ratio): non-orthonormal, but symmetrically treats all parts.

• pc_basis(), pb_basis(), pw_basis() – domain-specific and data-driven bases:

  • PC basis: based on principal component analysis of log-ratio coordinates.
  • PB basis (Principal balances): variability explain by balances.
  • PW (Pairwise Log-Ratios): pairwise comparisons.

• coordinates(x, basis): expresses a composition x in coordinates with respect to a given basis.

• composition(z, basis): reconstructs a composition from coordinates z and the associated basis.

Example

library(coda.base)

# Define a simple 3-part composition
x <- c('a' = 0.2, 'b' = 0.3, 'c' = 0.5)

# Create an ILR basis and express x in ILR coordinates
B <- ilr_basis(x)
h <- coordinates(x, B)  
h

# Recover the original composition
composition(h, B)

Installation

You can install the development version from GitHub:

# Install development version from GitHub
remotes::install_github("mcomas/coda.base")

and the cran version with:

# Install release version from CRAN
install.packages("coda.base")

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.