NEWS

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nexus 0.4.0.9000

nexus 0.4.0

New classes and methods

• Add ReferenceGroups, GroupedComposition and GroupedLogRatio classes to represent grouped data.
• Add group(), ungroup(), group_levels(), group_names(), group_indices(), group_rows(), group_length(), group_size(), group_extract(), group_split() and is_grouped() to work with grouped data.
• Add transform_lr(), transform_clr(), transform_alr(), transform_ilr(), transform_plr() and transform_inverse() methods for GroupedComposition and GroupedLogRatio objects.
• Add is_composition(), is_logratio() and is_grouped() to check if an object is from a specific class.
• Add pairs() to display a matrix of ternary plots.

Enhancements

• as_composition() gained a new autodetect argument to enable/disable automatic detection of numeric variables.

Breaking changes

• Redesign the internal mechanism for grouping data.
• hist() now produces a single histogram.
• plot(<LogRatio>) produces a scatter plot instead of a density plot.
• Rename the plot() method for the CompositionMatrix class to pairs().

nexus 0.3.0 (2024-09-03)

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 (2024-02-26)

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 (2023-11-29)

• First release.