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nexus 0.3.0.9000

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.

Breaking changes

  • Redesign the internal mechanism for grouping data.
  • hist() now produces a single histogram.

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.