NEWS.md

In nexus: Sourcing Archaeological Materials by Chemical Composition

nexus 0.3.0

New classes and methods

• Add transformation methods for LogRatio objects (clr <-> alr, clr -> ilr, alr -> ilr).
• Add condense() to compute compositional mean of data subsets.
• Add pip() to compute proportionality index of parts.
• Add rbind() method for CompositionMatrix objects.
• Add show() methods for LogRatio objects.
• Add is_element_major(), is_element_minor(), is_element_trace() and is_oxide() methods for CompositionMatrix objects.
• Add variance() and variance_total() to compute (total) variance.

Enhancements

• Add example datasets.
• Improve bar chart rendering.

Bugfixes & changes

• Fix pca() for LogRatio objects (default arguments were not passed to the internal method).

Internals

• Store groups as factor instead of character.

Breaking changes

• [ always returns a CompositionMatrix object by default, even if only one row/column is accessed.
• Remove samples slot in all classes.
• Remove as_features().
• Remove metrix_var() and metric_sd().
• Remove the base argument of transform_ilr().
• Rename get_totals() and set_totals() to totals().
• Rename get_groups() and get_groups() to groups().
• Rename outliers() to detect_outlier() and redefine methods.
• Rewrite plot() method for OutlierIndex object.

nexus 0.2.0

New classes and methods

• Add hist() methods to plot ILR histograms.
• Add quantile() methods for compositional data matrix.
• Add split() methods to divide into groups.

Enhancements

• transform_ilr() gained a new argument allowing the specify the base of the transformation.
• barplot() gained a new argument to display a legend.

Internals

• List dimensio in Depends.

nexus 0.1.0

• First release.

nexus documentation built on Sept. 11, 2024, 6:43 p.m.