Removed old recover_aug_rows() definition to resolve merge conflict

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ordr
 Title: A Tidyverse Extension for Ordinations and Biplots
-Version: 0.1.1.0001
+Version: 0.1.1.0002
 Authors@R: c(
   person("Jason Cory", "Brunson", email = "[email protected]",
     role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3126-9494")),
@@ -32,6 +32,7 @@ Depends:
     ggplot2
 Imports:
     rlang,
+    cli,
     stringr,
     tidyselect,
     scales,
@@ -49,6 +50,7 @@ Suggests:
     gridExtra,
     MASS,
     mlpack,
+    ddalpha,
     knitr,
     rmarkdown
 License: GPL-3
@@ -62,6 +64,8 @@ Collate:
     'aaa-.r'
     'biplot-key.r'
     'biplot.r'
+    'coord-rect.r'
+    'coord-scaffold.r'
     'data.r'
     'dplyr-verbs.r'
     'utils.r'
@@ -73,9 +77,12 @@ Collate:
     'fun-lra.r'
     'fun-wrap.r'
     'geom-axis.r'
+    'geom-bagplot.r'
+    'geom-interpolation.r'
     'geom-intervals.r'
     'geom-isoline.r'
     'geom-origin.r'
+    'geom-rule.r'
     'geom-text-radiate.r'
     'geom-utils.r'
     'geom-vector.r'
@@ -100,13 +107,18 @@ Collate:
     'ord-tidiers.r'
     'ordinate.r'
     'ordr.r'
-    'stat-center.r'
     'stat-chull.r'
+    'stat-depth.r'
+    'stat-bagplot.r'
+    'stat-center.r'
     'stat-cone.r'
     'stat-matrix.r'
+    'stat-referent.r'
+    'stat-projection.r'
+    'stat-rule.r'
     'stat-scale.r'
     'stat-spantree.r'
-    'themes.r'
+    'theme-scaffold.r'
     'zzz-biplot-geoms.r'
     'zzz-biplot-stats.r'
     'zzz.r'

NAMESPACE

@@ -23,6 +23,7 @@ S3method(biplot,tbl_ord)
 S3method(dim,tbl_ord)
 S3method(format,tbl_ord)
 S3method(fortify,tbl_ord)
+S3method(ggplot_add,LayerRef)
 S3method(glance,tbl_ord)
 S3method(lda_ord,data.frame)
 S3method(lda_ord,default)
@@ -182,33 +183,61 @@ S3method(screeplot,tbl_ord)
 S3method(stats::model.frame,lda_ord)
 S3method(tidy,tbl_ord)
 export("%>%")
+export(CoordRect)
+export(CoordScaffold)
 export(GeomAxis)
+export(GeomBagplot)
+export(GeomInterpolation)
 export(GeomIsoline)
 export(GeomLineranges)
 export(GeomOrigin)
 export(GeomPointranges)
+export(GeomRule)
 export(GeomTextRadiate)
 export(GeomUnitCircle)
 export(GeomVector)
+export(StatBagplot)
 export(StatCenter)
 export(StatChull)
 export(StatCols)
+export(StatColsBagplot)
 export(StatColsCenter)
 export(StatColsChull)
 export(StatColsCone)
+export(StatColsDensity2d)
+export(StatColsDensity2dFilled)
+export(StatColsDepth)
+export(StatColsDepthFilled)
 export(StatColsEllipse)
+export(StatColsPeel)
+export(StatColsProjection)
+export(StatColsRule)
 export(StatColsScale)
 export(StatColsSpantree)
 export(StatColsStar)
 export(StatCone)
+export(StatDepth)
+export(StatDepthFilled)
+export(StatPeel)
+export(StatProjection)
+export(StatReferent)
 export(StatRows)
+export(StatRowsBagplot)
 export(StatRowsCenter)
 export(StatRowsChull)
 export(StatRowsCone)
+export(StatRowsDensity2d)
+export(StatRowsDensity2dFilled)
+export(StatRowsDepth)
+export(StatRowsDepthFilled)
 export(StatRowsEllipse)
+export(StatRowsPeel)
+export(StatRowsProjection)
+export(StatRowsRule)
 export(StatRowsScale)
 export(StatRowsSpantree)
 export(StatRowsStar)
+export(StatRule)
 export(StatScale)
 export(StatSpantree)
 export(StatStar)
@@ -219,12 +248,21 @@ export(cbind_cols)
 export(cbind_rows)
 export(cmdscale_ord)
 export(confer_inertia)
+export(coord_rect)
+export(coord_scaffold)
+export(coord_square)
 export(draw_key_crosslines)
 export(draw_key_crosspoint)
 export(draw_key_line)
 export(eigen_ord)
 export(geom_axis)
+export(geom_bagplot)
 export(geom_cols_axis)
+export(geom_cols_bagplot)
+export(geom_cols_contour)
+export(geom_cols_density_2d)
+export(geom_cols_density_2d_filled)
+export(geom_cols_interpolation)
 export(geom_cols_isoline)
 export(geom_cols_label)
 export(geom_cols_label_repel)
@@ -233,16 +271,23 @@ export(geom_cols_path)
 export(geom_cols_point)
 export(geom_cols_pointranges)
 export(geom_cols_polygon)
+export(geom_cols_rule)
 export(geom_cols_text)
 export(geom_cols_text_radiate)
 export(geom_cols_text_repel)
 export(geom_cols_vector)
+export(geom_interpolation)
 export(geom_isoline)
 export(geom_label_repel)
 export(geom_lineranges)
 export(geom_origin)
 export(geom_pointranges)
 export(geom_rows_axis)
+export(geom_rows_bagplot)
+export(geom_rows_contour)
+export(geom_rows_density_2d)
+export(geom_rows_density_2d_filled)
+export(geom_rows_interpolation)
 export(geom_rows_isoline)
 export(geom_rows_label)
 export(geom_rows_label_repel)
@@ -251,10 +296,12 @@ export(geom_rows_path)
 export(geom_rows_point)
 export(geom_rows_pointranges)
 export(geom_rows_polygon)
+export(geom_rows_rule)
 export(geom_rows_text)
 export(geom_rows_text_radiate)
 export(geom_rows_text_repel)
 export(geom_rows_vector)
+export(geom_rule)
 export(geom_text_radiate)
 export(geom_text_repel)
 export(geom_unit_circle)
@@ -267,13 +314,17 @@ export(get_negation)
 export(get_rows)
 export(ggbiplot)
 export(glance)
+export(is.sync)
 export(is.tbl_ord)
 export(is_tbl_ord)
 export(lda_ord)
 export(left_join_cols)
 export(left_join_rows)
 export(lra)
 export(make_tbl_ord)
+export(maxpp)
+export(minabspp)
+export(minpp)
 export(mutate_cols)
 export(mutate_rows)
 export(negate_ord)
@@ -298,30 +349,55 @@ export(revert_conference)
 export(revert_negation)
 export(select_cols)
 export(select_rows)
+export(stat_bagplot)
 export(stat_center)
 export(stat_chull)
 export(stat_cols)
+export(stat_cols_bagplot)
 export(stat_cols_center)
 export(stat_cols_chull)
 export(stat_cols_cone)
+export(stat_cols_density_2d)
+export(stat_cols_density_2d_filled)
+export(stat_cols_depth)
+export(stat_cols_depth_filled)
 export(stat_cols_ellipse)
+export(stat_cols_peel)
+export(stat_cols_projection)
+export(stat_cols_rule)
 export(stat_cols_scale)
 export(stat_cols_spantree)
 export(stat_cols_star)
 export(stat_cone)
+export(stat_depth)
+export(stat_depth_filled)
+export(stat_peel)
+export(stat_projection)
+export(stat_referent)
 export(stat_rows)
+export(stat_rows_bagplot)
 export(stat_rows_center)
 export(stat_rows_chull)
 export(stat_rows_cone)
+export(stat_rows_density_2d)
+export(stat_rows_density_2d_filled)
+export(stat_rows_depth)
+export(stat_rows_depth_filled)
 export(stat_rows_ellipse)
+export(stat_rows_peel)
+export(stat_rows_projection)
+export(stat_rows_rule)
 export(stat_rows_scale)
 export(stat_rows_spantree)
 export(stat_rows_star)
+export(stat_rule)
 export(stat_scale)
 export(stat_spantree)
 export(stat_star)
 export(svd_ord)
+export(sync)
 export(theme_biplot)
+export(theme_scaffold)
 export(tidy)
 export(transmute_cols)
 export(transmute_rows)
@@ -342,6 +418,8 @@ importFrom(ggrepel,GeomLabelRepel)
 importFrom(ggrepel,GeomTextRepel)
 importFrom(ggrepel,geom_label_repel)
 importFrom(ggrepel,geom_text_repel)
+importFrom(ggrepel,position_nudge_repel)
+importFrom(grDevices,chull)
 importFrom(graphics,plot)
 importFrom(magrittr,"%>%")
 importFrom(rlang,"%||%")
@@ -353,6 +431,7 @@ importFrom(rlang,expr)
 importFrom(rlang,is_empty)
 importFrom(rlang,is_formula)
 importFrom(rlang,is_function)
+importFrom(rlang,list2)
 importFrom(rlang,set_names)
 importFrom(stats,.checkMFClasses)
 importFrom(stats,.getXlevels)

NEWS.md

@@ -1,13 +1,94 @@
 # next version
 
-## debugged axis geom
+## infrastructure and standards
 
-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()`.
+### wrapper defaults
+
+Previously, `lda_ord()` mimicked `MASS::lda()` in defaulting the retrieval parameters `ret.x` and `ret.grouping` to `FALSE`.
+Because they are so important to analysis and especially to biplots, they now default to `TRUE`.
+
+### unit tests
+
+Unit tests have been written for all ggproto shortcuts.
+
+## upgrades to the biplot chassis
 
-## axis harmonizers
+### axis harmonizers
 
 Multiple harmonizers are now available for scaling secondary axes. That recommended by Gower, Gardner--Lubbe, and Le Roux (2011) is the default, but the user can still specify a numeric scale instead.
 
+### GDA-geared coordinate systems
+
+Two new coordinate systems provide control over the aspect ratio of the plotting window without compromising that of the (artificial) coordinate axes:
+`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.
+
+### scaffold theme
+
+The 'biplot' theme has been renamed 'scaffold', with an alias for backward compatibility.
+
+### standardized and restrictive elements parameter (breaking change)
+
+The `elements` parameter is now standardized across all statistical transformations (through the code generation process) and accepts more restrictive options:
+The value is argument-matched to `"active"`, `"score"`, or `"structure"`; these options may expand as additional supplementary elements are introduced.
+Moreover, the former default `"all"` is no longer accepted, which forecloses the trick of passing the element type to an aesthetic, e.g. `size = .element == "active"`, as had been used in several examples.
+
+## up( or down)grades to existing plot layers
+
+### combined vector and radiating text geom (breaking change)
+
+The 'vector' and 'text_radiate' geoms have been combined.
+The shortcut `geom_text_radiate()` is deprecated, and `geom_vector()` generates radiating labels by default.
+
+### debugged axis geom
+
+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()`.
+
+### reconciliation of summary functions
+
+The 'center' and 'star' stats now follow the 'summary' stat convention of using `fun`, so `fun.center` is deprecated.
+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.
+
+### revamped handling of secondary aesthetics (breaking change)
+
+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.
+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}.
+This induces some breaking changes due to the renaming of most, and the removal of some, such parameters.
+
+### deprecation of scale stat
+
+The simple and experimental `StatScale` has been deprecated.
+
+## new plot layers
+
+### addition geom
+
+A new 'interpolation' geometric element layer renders either of two methods of vector addition to interpolate the position---on the existing ordination and its biplot---of a new row or column of the original data matrix.
+
+### referential stats
+
+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.
+
+### projection stat
+
+The 'projection' referential stat prepares segment endpoints between `x,y` positions and their projections on axes defined by the reference data. It is a natural graphical element for predictive biplots of ordination models of continuous data.
+
+### rule stat
+
+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.
+
+### peel stat
+
+A new 'peel' statistical transformation computes nested convex hulls containing specified fractions of data.
+
+### depth stat
+
+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.
+
+### adapted density stat & geom
+
+Aided by element standardization, the classic `density_2d` statistical transformation and geometric construction are adapted to biplots.
+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()`.
+
 # ordr 0.1.1
 
 ## `linewidth` aesthetic (breaking change)