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As with the `data` argument, the `referent` argument of `stat_referent()` can now be passed a function, which will be evaluated at `data` to obtain the reference data for the plot layer.
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As with the `data` argument, the `referent` argument of `stat_referent()` can
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now be passed a function, which will be evaluated at `data` to obtain the
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reference data for the plot layer.
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The evaluation is done during addition of a layer of class `LayerRef`.
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# gggda 0.1.1
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This patch fixes a bug in the peel stat and adds unit tests for it and the scale stat.
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This patch fixes a bug in the peel stat and adds unit tests for it and the scale
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stat.
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To resolve outstanding CRAN checks, a cross-reference to {ordr} has been replaced with a URL and {dplyr} and {tidyr} functions previously called using the double-colon operator have been imported instead.
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To resolve outstanding CRAN checks, a cross-reference to {ordr} has been
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replaced with a URL and {dplyr} and {tidyr} functions previously called using
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the double-colon operator have been imported instead.
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# gggda 0.1.0
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The inaugural version of {gggda} was spun off the post-v0.1.1 development version of {ordr}.
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Upgrades to {ordr} components since that release that are included in {gggda} are listed here.
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The inaugural version of {gggda} was spun off the post-v0.1.1 development
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version of {ordr}.
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Upgrades to {ordr} components since that release that are included in {gggda}
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are listed here.
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## infrastructure and standards
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@@ -24,30 +31,44 @@ Unit tests have been written for all ggproto shortcuts.
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### GDA-geared coordinate systems
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Two new coordinate systems provide control over the aspect ratio of the plotting window without compromising that of the (artificial) coordinate axes:
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`GeomRect` (alias `GeomSquare`) extends `GeomFixed` with an `window_ratio` parameter for the plotting window, while `GeomBiplot` removes the `ratio` parameter and forces the coordinate axes to have aspect ratio 1.
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Two new coordinate systems provide control over the aspect ratio of the plotting
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window without compromising that of the (artificial) coordinate axes:
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`GeomRect` (alias `GeomSquare`) extends `GeomFixed` with an `window_ratio`
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parameter for the plotting window, while `GeomBiplot` removes the `ratio`
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parameter and forces the coordinate axes to have aspect ratio 1.
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## up( or down)grades to existing plot layers
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### combined vector and radiating text geom (breaking change)
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The 'vector' and 'text_radiate' geoms have been combined.
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The shortcut `geom_text_radiate()` is deprecated, and `geom_vector()` generates radiating labels by default.
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The shortcut `geom_text_radiate()` is deprecated, and `geom_vector()` generates
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radiating labels by default.
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### debugged axis geom
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The 'axis' and 'isoline' geoms hit trouble when one or more points lay at the origin (`x^2 + y^2 == 0`). These cases have now been removed in `setup_data()`.
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The 'axis' and 'isoline' geoms hit trouble when one or more points lay at the
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origin (`x^2 + y^2 == 0`). These cases have now been removed in `setup_data()`.
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### reconciliation of summary functions
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The 'center' and 'star' stats now follow the 'summary' stat convention of using `fun`, so `fun.center` is deprecated.
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Additionally, `fun.ord` accepts a function that summarizes the columns of a matrix, which accommodates summaries like the depth median that do not decompose along orthogonal axes.
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The 'center' and 'star' stats now follow the 'summary' stat convention of using
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`fun`, so `fun.center` is deprecated.
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Additionally, `fun.ord` accepts a function that summarizes the columns of a
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matrix, which accommodates summaries like the depth median that do not decompose
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along orthogonal axes.
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### revamped handling of secondary aesthetics (breaking change)
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Previously, underscore-separated parameters like `label_colour` were used to specify secondary aesthetics, i.e. aesthetics for graphical objects other than those considered "primary" for the layer.
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Their behavior has been debugged by mimicking the use of period-separated parameters like `label.colour` in {ggplot2} v3.5.1, except for the new bagplot geom, for which their behavior is based on that of `geom_boxplot()` in the current development version of {ggplot2}.
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This induces some breaking changes due to the renaming of most, and the removal of some, such parameters.
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Previously, underscore-separated parameters like `label_colour` were used to
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specify secondary aesthetics, i.e. aesthetics for graphical objects other than
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those considered "primary" for the layer.
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Their behavior has been debugged by mimicking the use of period-separated
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parameters like `label.colour` in {ggplot2} v3.5.1, except for the new bagplot
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geom, for which their behavior is based on that of `geom_boxplot()` in the
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current development version of {ggplot2}.
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This induces some breaking changes due to the renaming of most, and the removal
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of some, such parameters.
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### deprecation of scale stat
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### referential stats
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A new statistical transformation serves to parent specific "referential stats", meaning those that depend on non-inherited (in this setting, positional) data to transform the inherited data. The reference data are passed to the new `referent` parameter. The new stat is coupled with an additional `LayerRef` class that enables `ggplot_add()` to pass the inherited positional aesthetics to `$setup_params()`. Biplot-specific `stat_*_*()` shortcuts accept additional argument types to `referent` that result in the opposite matrix factor being used as reference data.
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A new statistical transformation serves to parent specific "referential stats",
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meaning those that depend on non-inherited (in this setting, positional) data to
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transform the inherited data. The reference data are passed to the new
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`referent` parameter. The new stat is coupled with an additional `LayerRef`
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class that enables `ggplot_add()` to pass the inherited positional aesthetics to
argument types to `referent` that result in the opposite matrix factor being
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used as reference data.
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### rule stat
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A new 'rule' statistical transformation computes additional position aesthetics that the 'axis' geom uses to limit and offset axes. The stat is referential and expects a set of functions that compute limits `lower` and `upper` along the axes and `yintercept` and `xintercept` associated with offset axes. The 'axis' geom preprocesses these aesthetics to rule endpoints `xmin,ymin,xmax,ymax` and offset vectors `xend,yend` to force the plotting window to contain the limited axis segments or, if the axes remain lines, the offsets where they are centered.
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A new 'rule' statistical transformation computes additional position aesthetics
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that the 'axis' geom uses to limit and offset axes. The stat is referential and
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expects a set of functions that compute limits `lower` and `upper` along the
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axes and `yintercept` and `xintercept` associated with offset axes. The 'axis'
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geom preprocesses these aesthetics to rule endpoints `xmin,ymin,xmax,ymax` and
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offset vectors `xend,yend` to force the plotting window to contain the limited
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axis segments or, if the axes remain lines, the offsets where they are centered.
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### peel stat
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A new 'peel' statistical transformation computes nested convex hulls containing specified fractions of data.
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A new 'peel' statistical transformation computes nested convex hulls containing
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specified fractions of data.
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### depth stat
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A new 'depth' statistical transformation estimates depth across a grid and is paired with `GeomContour` to produce depth contours, which can be used to plot alpha bags.
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A new 'depth' statistical transformation estimates depth across a grid and is
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paired with `GeomContour` to produce depth contours, which can be used to plot
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alpha bags.
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### adapted density stat & geom
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Aided by element standardization, the classic `density_2d` statistical transformation and geometric construction are adapted to biplots.
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Currently, source code generation does not respect fixed parameters passed to `layer()` by the `stat_*()` and `geom_*()` shortcuts; as a consequence, `contour = TRUE` must be manually passed to `geom_*_density_2d()`.
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Aided by element standardization, the classic `density_2d` statistical
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transformation and geometric construction are adapted to biplots.
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Currently, source code generation does not respect fixed parameters passed to
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`layer()` by the `stat_*()` and `geom_*()` shortcuts; as a consequence, `contour
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= TRUE` must be manually passed to `geom_*_density_2d()`.
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# ordr 0.1.1
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## `linewidth` aesthetic (breaking change)
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An upcoming release of {ggplot2} controls stroke width using the new `linewidth` aesthetic rather than `size`. This {ordr} release adapts to this change internally for `GeomUnitCircle` and by updating row and column layers automatically adapted from {ggplot2}. (#50)
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An upcoming release of {ggplot2} controls stroke width using the new `linewidth`
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aesthetic rather than `size`. This {ordr} release adapts to this change
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internally for `GeomUnitCircle` and by updating row and column layers
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automatically adapted from {ggplot2}. (#50)
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## class 'eigen'
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Methods are added for the 'eigen' class returned by `eigen()`, and the internal `eigen_ord()` function and its methods are updated accordingly.
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Methods are added for the 'eigen' class returned by `eigen()`, and the internal
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`eigen_ord()` function and its methods are updated accordingly.
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## list tidiers (breaking change)
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The previous version extended the 'list' method for {broom}'s `tidy()` and `glance()` functions to recognize the output of `cmdscale()` and of `cancor()`.
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These have been spun off to a nascent helper package, {broom.list}, to reduce size and prevent attachment warnings.
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The previous version extended the 'list' method for {broom}'s `tidy()` and
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`glance()` functions to recognize the output of `cmdscale()` and of `cancor()`.
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These have been spun off to a nascent helper package, {broom.list}, to reduce
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size and prevent attachment warnings.
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# ordr 0.1.0
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In addition to minor changes, the following substantive changes are made from v0.0.2:
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In addition to minor changes, the following substantive changes are made from
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v0.0.2:
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## augmentation
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The column names of `augment_ord()` and `tidy()` outputs are no longer prefixed by periods.
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The column names of `augment_ord()` and `tidy()` outputs are no longer prefixed
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by periods.
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## list tidiers
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A new list tidier for `cancor()` output is introduced.
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## negation
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Tools to negate a subset of artificial dimensions, adapted from the sandboxed set of alignment tools, are provided.
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Tools to negate a subset of artificial dimensions, adapted from the sandboxed
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set of alignment tools, are provided.
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## convenience function
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The `ordinate()` function is now a generic with methods for four data classes.
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## ggbiplot
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The logical `prediction` parameter is replaced with the character-valued `axis.type`, based on the `ax.type` parameter used in {UBbipl} (Gower, Gardner--Lubbe, & le Roux, 2011).
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The logical `prediction` parameter is replaced with the character-valued
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`axis.type`, based on the `ax.type` parameter used in {UBbipl} (Gower,
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Gardner--Lubbe, & le Roux, 2011).
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## tests
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Unit tests are overhauled to remove contexts, omit ad hoc tests, standardize method tests, and cover additional methods.
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Unit tests are overhauled to remove contexts, omit ad hoc tests, standardize
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method tests, and cover additional methods.
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## documentation
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The term 'accessor', used to refer to S3 class methods to recover standardized model components, has been changed to 'recoverer'.
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The term 'accessor', used to refer to S3 class methods to recover standardized
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model components, has been changed to 'recoverer'.
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# ordr 0.0.2
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This pre-release makes several substantive changes in preparation for CRAN submission.
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This pre-release makes several substantive changes in preparation for CRAN
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submission.
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## element types
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Annotation of active and supplementary elements is standardized: The character augmentation `.element` replaces the logical `.supplement`, and class methods either omit it entirely (when all retrieved elements are active) or include it in both row and column augmentation (when either includes supplementary elements). The value of `.element` is either 'active' or a type of supplement, e.g. 'score'.
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Annotation of active and supplementary elements is standardized: The character
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augmentation `.element` replaces the logical `.supplement`, and class methods
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either omit it entirely (when all retrieved elements are active) or include it
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in both row and column augmentation (when either includes supplementary
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elements). The value of `.element` is either 'active' or a type of supplement,
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e.g. 'score'.
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## dependencies
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Extraneous dependencies are dropped to reduce overhead. This takes two forms:
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1. Methods for classes from specialty (lower-priority) packages ({candisc} and {ca}) are moved to {ordr.extra} and replaced with methods for classes from higher-priority packages ({stats} and {MASS}).
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1. Methods for classes from specialty (lower-priority) packages ({candisc} and
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{ca}) are moved to {ordr.extra} and replaced with methods for classes from
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higher-priority packages ({stats} and {MASS}).
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2. One-off uses of specialty packages for examples and vignettes are replaced.
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## documentation
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The `Description` field in DESCRIPTION is expanded and documentation throughout is slightly revised, including some new references.
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The `Description` field in DESCRIPTION is expanded and documentation throughout
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is slightly revised, including some new references.
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# ordr 0.0.1
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This is a pre-release in anticipation of a first CRAN submission.
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Upgrades between this pre-release and CRAN submission will focus on addressing issues.
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Upgrades between this pre-release and CRAN submission will focus on addressing
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