Changelog

Source: NEWS.md

coda.base 1.0.7 (Release date: 2026-05-12)

• dist_coda() now accepts method = "L2" as an alias for the Euclidean distance.
• The partial principal-balance search validates grouped inputs more thoroughly and improves the handling of tabu-search neighbourhoods.
• Additional tests cover distance aliases, basis construction and partial tabu-search edge cases.
• The pkgdown site now uses Bootstrap 5 and includes a redesigned logo, favicons and a revised Get Started vignette.

coda.base 1.0.6 (Release date: 2026-05-08)

CRAN release: 2026-05-08

• Added the standard compositional operations closure(), perturbation() and powering().
• Added dist_coda() for Aitchison, angular, L1 and Euclidean distances between compositions.
• Added exact, constrained and tabu-search methods for partial principal balances: partial_pb_exact(), partial_pb_constrained() and partial_pb_tabu_search().
• Added pb_tabu_search() to construct a sequential binary partition by tabu search, together with random_composition_with_fixed_pb() for simulation.
• Extended pb_basis() with the tabu-search method and improved the C++ implementation of principal-balance searches.
• Expanded validation and tests for compositional operations, distances, zero replacement and tabu-search neighbourhoods.
• Corrected the statistitian_time data set name to statistician_time.

coda.base 1.0.5 (Release date: 2026-03-03)

CRAN release: 2026-03-04

• Reworked the basis and coordinate code, with stronger checks for dimensions, names and invalid compositions.
• Added cdp_basis() and conditional_obasis() to the public API.
• Added gen_coda_with_zeros_and_missings() for generating data sets used to assess zero and missing-value replacement methods.
• Improved coda_replacement() and the conditional orthonormal-basis calculations used for zero and missing-value imputation.
• Improved sbp_basis(), constrained principal balances and the C++ principal-balance implementation.
• plot_balance() can display statistics associated with balances.
• Optimised and reorganised the C++ code and expanded the basis tests.

coda.base 1.0.4 (Release date: 2025-09-20)

• Changed the sign convention of CoDaPack bases to agree with CoDaPack.

coda.base 1.0.3 (Release date: 2025-07-02)

CRAN release: 2025-07-02

• Improved completion of sequential binary partitions in sbp_basis().
• Improved constrained principal-balance calculations and their handling of subcompositions.

coda.base 1.0.2 (Release date: 2025-05-07)

• Added the kilauea_iki compositional data set and its documentation.
• Improved documentation for zero replacement and coordinate transformations.
• Improved dimension checks for pairwise bases and composition reconstruction.

coda.base 1.0.0 (Release date: 2025-05-02)

CRAN release: 2025-05-02

• Added coda_replacement() for imputing rounded zeros and missing values in compositional data.
• Added conditional orthonormal-basis calculations used by the imputation procedure.
• Reorganised basis, coordinate and constrained principal-balance code, with more consistent argument validation and naming.
• Updated the package documentation and test suite for the 1.0 release.

coda.base 0.5.5 (Release date: 2023-11-25)

CRAN release: 2023-11-25

• Added direct coordinate helpers alr_c(), clr_c(), ilr_c() and olr_c().
• Added olr_basis() and support for orthonormal log-ratio coordinates in coordinates() and composition().
• Extended variation_array() with optional log-ratio means and changed its defaults to return the variation matrix directly.
• Improved printing of coordinate objects and preservation of basis metadata.

coda.base 0.5.4 (Release date: 2023-03-01)

• Added a collection of documented compositional data sets, including alimentation, blood_mn, bmi_activity, eurostat_employment, foraminiferals, house_expend, mammals_milk, milk_cows, montana, petrafm, pollen, serprot, statistitian_time and weibo_hotels.
• plot_balance() now uses balance names in dendrogram labels.
• Fixed completion of incomplete sequential binary partitions in sbp_basis().
• Removed cc_basis() because its results did not match the intended method; it was redesigned and restored in a later release.

coda.base 0.5.3 (Release date: 2023-02-08)

• sbp_basis() can complete an incomplete sequential binary partition to obtain a full basis.

coda.base 0.5.2 (Release date: 2022-07-14)

CRAN release: 2022-07-18

• Basis constructors consistently return standard R matrices; sparse matrices are used internally where they improve performance.
• Updated the minimum RcppArmadillo requirement for the compiled code.

coda.base 0.5.1 (Release date: 2022-07-07)

• Added the Wilks statistic as a criterion for canonical-correlation balances.

coda.base 0.4.3

• center() and gmean() functions incorporated.

coda.base 0.4.2

• Pairwise default name changed to lr instead of alr.
• Sparse matrices are used for logcontrast matrices of balances.
• Problem with constrained principal balances detected and solved.

coda.base 0.3.2 (Release date: 2022-03-13)

• coord() and comp() are included as a shorter names of coordinates() and composition().
• Basis names taken from composition.
• Coordinates based on pairwise log-ratios available with pairwise_basis() or basis = ‘pw’ in function coordinates().
• Parameter label removed in function coordinates().

coda.base 0.3.1

CRAN release: 2020-05-14

• PB constrained approximation available. Adaptation of code provided by J.A.Martín-Fernández.
• PB exact algorithm rewritten to improve performance.
• PB local search algorithm removed.

coda.base 0.2.2

CRAN release: 2020-04-16

• MASS dependence removed
• Code reorganised to avoid repetition.

coda.base 0.2.1

CRAN release: 2019-07-02

• ?_basis functions always return a matrix
• consistencies between methods improved

coda.base 0.1.12 (Release date: 2018-04-15)

CRAN release: 2019-04-15

• coordinates function keeps row.names attribute
• Principal components calculations are done using svd function which is faster than princomp
• sbp_basis function does not need package to be loaded, can run as coda.base::sbp_basis()

coda.base 0.1.11 (Release date: 2018-12-23)

CRAN release: 2019-01-15

• Principal components coordinates uncentered.
• Sequential binary partition can be defined using a matrix with -1,0 and 1’s.
• CoDaPack’s basis included.
• A vignette explaining how to build coordinates has been included.

coda.base 0.1.10 (Release date: 2018-08-03)

CRAN release: 2018-08-06

• Principal Balances included as direct method in coordinates function.
• Coordinates function filters non-valid compositions.

coda.base 0.1.9 (Release date: 2018-05-03)

CRAN release: 2018-05-09

• Modifications included to rcran policies.

coda.base 0.1.8 (Release date: 2017-12-03)

CRAN release: 2017-12-03

• Exact algorithm for Principal Balances included.
• Bug in lsearch base in principal components solved.

coda.base 0.1.7 (Release date: 2017-08-25)

CRAN release: 2017-09-26

• Problem with function composition using ‘clr’ basis solved.
• ‘coda.base.basis’ option included to hide the basis when printing the coordinates.
• New method which uses the principal components included in pb_basis.
• Documentaion improved.