A 'tidyverse' Extension for Ordinations and Biplots

---

Documentation for package ‘ordr’ version 0.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A B C D E F G I L M N O P Q R S T U V W

ordr-package

*ordr* package

-- A --

annotation	Annotate factors of 'tbl_ord' objects
as.matrix.tbl_ord	Access factors, coordinates, and metadata from ordination objects
as_tbl_ord	A unified ordination object class
as_tbl_ord.cancor_ord	Functionality for canonical correlations
as_tbl_ord.cmds_ord	Functionality for classical multidimensional scaling objects
as_tbl_ord.correspondence	Functionality for correspondence analysis ('correspondence') objects
as_tbl_ord.eigen	Functionality for eigen-decompositions
as_tbl_ord.eigen_ord	Functionality for eigen-decompositions
as_tbl_ord.factanal	Functionality for factor analysis ('factanal') objects
as_tbl_ord.kmeans	Functionality for k-means clustering ('kmeans') objects
as_tbl_ord.lda	Functionality for linear discriminant analysis ('lda') objects
as_tbl_ord.lda_ord	Functionality for linear discriminant analysis ('lda') objects
as_tbl_ord.lm	Functionality for linear model objects
as_tbl_ord.lra	Functionality for log-ratio analysis ('lra') objects
as_tbl_ord.mca	Functionality for multiple correspondence analysis ('mca') objects
as_tbl_ord.prcomp	Functionality for principal components analysis ('prcomp') objects
as_tbl_ord.princomp	Functionality for principal components analysis ('princomp') objects
as_tbl_ord.svd_ord	Functionality for singular value decompositions
as_tbl_ord.tbl_ord	A unified ordination object class
augmentation	Augment factors and coordinates of 'tbl_ord' objects
augment_ord	Augment factors and coordinates of 'tbl_ord' objects

-- B --

biplot-geoms	Convenience geoms for row and column matrix factors
biplot-stats	Convenience stats for row and column matrix factors
biplot.lra	Log-ratio analysis

-- C --

cancor_ord	Wrappers for lossy ordination methods
cbind_cols	*dplyr* verbs for tbl_ord factors
cbind_rows	*dplyr* verbs for tbl_ord factors
cmdscale_ord	Wrappers for lossy ordination methods
conference	Confer inertia to factors of a 'tbl_ord' object
confer_inertia	Confer inertia to factors of a 'tbl_ord' object

-- D --

dim.tbl_ord	Access factors, coordinates, and metadata from ordination objects
dplyr-verbs	*dplyr* verbs for tbl_ord factors
draw-key	Biplot key drawing functions
draw_key_crosslines	Biplot key drawing functions
draw_key_crosspoint	Biplot key drawing functions
draw_key_line	Biplot key drawing functions

-- E --

eigen_ord

Wrappers for lossy ordination methods

-- F --

format	Format a tbl_ord for printing
format.tbl_ord	Format a tbl_ord for printing
fortify.tbl_ord	Tidiers for 'tbl_ord' objects

-- G --

GeomAxis	ggproto classes created and adapted for ordr
GeomIsoline	ggproto classes created and adapted for ordr
GeomLineranges	ggproto classes created and adapted for ordr
GeomOrigin	ggproto classes created and adapted for ordr
GeomPointranges	ggproto classes created and adapted for ordr
GeomTextRadiate	ggproto classes created and adapted for ordr
GeomUnitCircle	ggproto classes created and adapted for ordr
GeomVector	ggproto classes created and adapted for ordr
geom_axis	Axes through the origin
geom_cols_axis	Convenience geoms for row and column matrix factors
geom_cols_isoline	Convenience geoms for row and column matrix factors
geom_cols_label	Convenience geoms for row and column matrix factors
geom_cols_label_repel	Convenience geoms for row and column matrix factors
geom_cols_lineranges	Convenience geoms for row and column matrix factors
geom_cols_path	Convenience geoms for row and column matrix factors
geom_cols_point	Convenience geoms for row and column matrix factors
geom_cols_pointranges	Convenience geoms for row and column matrix factors
geom_cols_polygon	Convenience geoms for row and column matrix factors
geom_cols_text	Convenience geoms for row and column matrix factors
geom_cols_text_radiate	Convenience geoms for row and column matrix factors
geom_cols_text_repel	Convenience geoms for row and column matrix factors
geom_cols_vector	Convenience geoms for row and column matrix factors
geom_isoline	Isolines (contour lines)
geom_lineranges	Intervals depicting ranges, usually about center points
geom_origin	Crosshairs or circle at the origin
geom_pointranges	Intervals depicting ranges, usually about center points
geom_rows_axis	Convenience geoms for row and column matrix factors
geom_rows_isoline	Convenience geoms for row and column matrix factors
geom_rows_label	Convenience geoms for row and column matrix factors
geom_rows_label_repel	Convenience geoms for row and column matrix factors
geom_rows_lineranges	Convenience geoms for row and column matrix factors
geom_rows_path	Convenience geoms for row and column matrix factors
geom_rows_point	Convenience geoms for row and column matrix factors
geom_rows_pointranges	Convenience geoms for row and column matrix factors
geom_rows_polygon	Convenience geoms for row and column matrix factors
geom_rows_text	Convenience geoms for row and column matrix factors
geom_rows_text_radiate	Convenience geoms for row and column matrix factors
geom_rows_text_repel	Convenience geoms for row and column matrix factors
geom_rows_vector	Convenience geoms for row and column matrix factors
geom_text_radiate	Text radiating outward from the origin
geom_unit_circle	Unit circle
geom_vector	Vectors from the origin
get_cols	Access factors, coordinates, and metadata from ordination objects
get_conference	Confer inertia to factors of a 'tbl_ord' object
get_coord	Access factors, coordinates, and metadata from ordination objects
get_inertia	Access factors, coordinates, and metadata from ordination objects
get_negation	Negation of ordination axes
get_rows	Access factors, coordinates, and metadata from ordination objects
ggbiplot	Biplots following the grammar of graphics
glance.tbl_ord	Tidiers for 'tbl_ord' objects
glass	Glass composition data

-- I --

is.tbl_ord	A unified ordination object class
is_tbl_ord	A unified ordination object class

-- L --

lda-ord	Augmented implementation of linear discriminant analysis
lda_ord	Augmented implementation of linear discriminant analysis
lda_ord.data.frame	Augmented implementation of linear discriminant analysis
lda_ord.default	Augmented implementation of linear discriminant analysis
lda_ord.formula	Augmented implementation of linear discriminant analysis
lda_ord.matrix	Augmented implementation of linear discriminant analysis
left_join_cols	*dplyr* verbs for tbl_ord factors
left_join_rows	*dplyr* verbs for tbl_ord factors
lra	Log-ratio analysis
lra-ord	Log-ratio analysis

-- M --

make_tbl_ord	A unified ordination object class
methods-cancor	Functionality for canonical correlations
methods-cmds	Functionality for classical multidimensional scaling objects
methods-correspondence	Functionality for correspondence analysis ('correspondence') objects
methods-eigen	Functionality for eigen-decompositions
methods-factanal	Functionality for factor analysis ('factanal') objects
methods-kmeans	Functionality for k-means clustering ('kmeans') objects
methods-lda	Functionality for linear discriminant analysis ('lda') objects
methods-lm	Functionality for linear model objects
methods-lra	Functionality for log-ratio analysis ('lra') objects
methods-mca	Functionality for multiple correspondence analysis ('mca') objects
methods-prcomp	Functionality for principal components analysis ('prcomp') objects
methods-princomp	Functionality for principal components analysis ('princomp') objects
methods-svd	Functionality for singular value decompositions
mutate_cols	*dplyr* verbs for tbl_ord factors
mutate_rows	*dplyr* verbs for tbl_ord factors

-- N --

negate_ord	Negation of ordination axes
negate_to_first_orthant	Negation of ordination axes
negation	Negation of ordination axes

-- O --

ordinate	Fit an ordination model to a data object
ordinate.array	Fit an ordination model to a data object
ordinate.data.frame	Fit an ordination model to a data object
ordinate.default	Fit an ordination model to a data object
ordinate.dist	Fit an ordination model to a data object
ordinate.table	Fit an ordination model to a data object
ordr	*ordr* package
ordr-ggproto	ggproto classes created and adapted for ordr
ord_aes	Biplots following the grammar of graphics

-- P --

plot.lra	Log-ratio analysis
plot.tbl_ord	Plot and biplot methods for 'tbl_ord' objects
predict.lda_ord	Augmented implementation of linear discriminant analysis
print.lra	Log-ratio analysis
print.tbl_ord	Format a tbl_ord for printing
pull_cols	*dplyr* verbs for tbl_ord factors
pull_factor	*dplyr* verbs for tbl_ord factors
pull_rows	*dplyr* verbs for tbl_ord factors

-- Q --

qswur_usa

U.S. university rankings

-- R --

recoverers	Access factors, coordinates, and metadata from ordination objects
recover_aug_cols	Augment factors and coordinates of 'tbl_ord' objects
recover_aug_cols.cancor_ord	Functionality for canonical correlations
recover_aug_cols.cmds_ord	Functionality for classical multidimensional scaling objects
recover_aug_cols.correspondence	Functionality for correspondence analysis ('correspondence') objects
recover_aug_cols.eigen_ord	Functionality for eigen-decompositions
recover_aug_cols.factanal	Functionality for factor analysis ('factanal') objects
recover_aug_cols.kmeans	Functionality for k-means clustering ('kmeans') objects
recover_aug_cols.lda	Functionality for linear discriminant analysis ('lda') objects
recover_aug_cols.lda_ord	Functionality for linear discriminant analysis ('lda') objects
recover_aug_cols.lm	Functionality for linear model objects
recover_aug_cols.lra	Functionality for log-ratio analysis ('lra') objects
recover_aug_cols.mca	Functionality for multiple correspondence analysis ('mca') objects
recover_aug_cols.mlm	Functionality for linear model objects
recover_aug_cols.prcomp	Functionality for principal components analysis ('prcomp') objects
recover_aug_cols.princomp	Functionality for principal components analysis ('princomp') objects
recover_aug_cols.svd_ord	Functionality for singular value decompositions
recover_aug_coord	Augment factors and coordinates of 'tbl_ord' objects
recover_aug_coord.cancor_ord	Functionality for canonical correlations
recover_aug_coord.cmds_ord	Functionality for classical multidimensional scaling objects
recover_aug_coord.correspondence	Functionality for correspondence analysis ('correspondence') objects
recover_aug_coord.eigen	Functionality for eigen-decompositions
recover_aug_coord.eigen_ord	Functionality for eigen-decompositions
recover_aug_coord.factanal	Functionality for factor analysis ('factanal') objects
recover_aug_coord.kmeans	Functionality for k-means clustering ('kmeans') objects
recover_aug_coord.lda	Functionality for linear discriminant analysis ('lda') objects
recover_aug_coord.lda_ord	Functionality for linear discriminant analysis ('lda') objects
recover_aug_coord.lm	Functionality for linear model objects
recover_aug_coord.lra	Functionality for log-ratio analysis ('lra') objects
recover_aug_coord.mca	Functionality for multiple correspondence analysis ('mca') objects
recover_aug_coord.mlm	Functionality for linear model objects
recover_aug_coord.prcomp	Functionality for principal components analysis ('prcomp') objects
recover_aug_coord.princomp	Functionality for principal components analysis ('princomp') objects
recover_aug_coord.svd_ord	Functionality for singular value decompositions
recover_aug_rows	Augment factors and coordinates of 'tbl_ord' objects
recover_aug_rows.cancor_ord	Functionality for canonical correlations
recover_aug_rows.cmds_ord	Functionality for classical multidimensional scaling objects
recover_aug_rows.correspondence	Functionality for correspondence analysis ('correspondence') objects
recover_aug_rows.eigen_ord	Functionality for eigen-decompositions
recover_aug_rows.factanal	Functionality for factor analysis ('factanal') objects
recover_aug_rows.glm	Functionality for linear model objects
recover_aug_rows.kmeans	Functionality for k-means clustering ('kmeans') objects
recover_aug_rows.lda	Functionality for linear discriminant analysis ('lda') objects
recover_aug_rows.lda_ord	Functionality for linear discriminant analysis ('lda') objects
recover_aug_rows.lm	Functionality for linear model objects
recover_aug_rows.lra	Functionality for log-ratio analysis ('lra') objects
recover_aug_rows.mca	Functionality for multiple correspondence analysis ('mca') objects
recover_aug_rows.mlm	Functionality for linear model objects
recover_aug_rows.prcomp	Functionality for principal components analysis ('prcomp') objects
recover_aug_rows.princomp	Functionality for principal components analysis ('princomp') objects
recover_aug_rows.svd_ord	Functionality for singular value decompositions
recover_cols	Access factors, coordinates, and metadata from ordination objects
recover_cols.cancor_ord	Functionality for canonical correlations
recover_cols.cmds_ord	Functionality for classical multidimensional scaling objects
recover_cols.correspondence	Functionality for correspondence analysis ('correspondence') objects
recover_cols.data.frame	Access factors, coordinates, and metadata from ordination objects
recover_cols.default	Access factors, coordinates, and metadata from ordination objects
recover_cols.eigen	Functionality for eigen-decompositions
recover_cols.eigen_ord	Functionality for eigen-decompositions
recover_cols.factanal	Functionality for factor analysis ('factanal') objects
recover_cols.kmeans	Functionality for k-means clustering ('kmeans') objects
recover_cols.lda	Functionality for linear discriminant analysis ('lda') objects
recover_cols.lda_ord	Functionality for linear discriminant analysis ('lda') objects
recover_cols.lm	Functionality for linear model objects
recover_cols.lra	Functionality for log-ratio analysis ('lra') objects
recover_cols.mca	Functionality for multiple correspondence analysis ('mca') objects
recover_cols.mlm	Functionality for linear model objects
recover_cols.prcomp	Functionality for principal components analysis ('prcomp') objects
recover_cols.princomp	Functionality for principal components analysis ('princomp') objects
recover_cols.svd_ord	Functionality for singular value decompositions
recover_conference	Confer inertia to factors of a 'tbl_ord' object
recover_conference.cancor_ord	Functionality for canonical correlations
recover_conference.cmds_ord	Functionality for classical multidimensional scaling objects
recover_conference.correspondence	Functionality for correspondence analysis ('correspondence') objects
recover_conference.default	Confer inertia to factors of a 'tbl_ord' object
recover_conference.eigen	Functionality for eigen-decompositions
recover_conference.eigen_ord	Functionality for eigen-decompositions
recover_conference.factanal	Functionality for factor analysis ('factanal') objects
recover_conference.lda	Functionality for linear discriminant analysis ('lda') objects
recover_conference.lda_ord	Functionality for linear discriminant analysis ('lda') objects
recover_conference.lra	Functionality for log-ratio analysis ('lra') objects
recover_conference.mca	Functionality for multiple correspondence analysis ('mca') objects
recover_conference.prcomp	Functionality for principal components analysis ('prcomp') objects
recover_conference.princomp	Functionality for principal components analysis ('princomp') objects
recover_conference.svd_ord	Functionality for singular value decompositions
recover_coord	Access factors, coordinates, and metadata from ordination objects
recover_coord.cancor_ord	Functionality for canonical correlations
recover_coord.cmds_ord	Functionality for classical multidimensional scaling objects
recover_coord.correspondence	Functionality for correspondence analysis ('correspondence') objects
recover_coord.data.frame	Access factors, coordinates, and metadata from ordination objects
recover_coord.default	Access factors, coordinates, and metadata from ordination objects
recover_coord.eigen	Functionality for eigen-decompositions
recover_coord.eigen_ord	Functionality for eigen-decompositions
recover_coord.factanal	Functionality for factor analysis ('factanal') objects
recover_coord.kmeans	Functionality for k-means clustering ('kmeans') objects
recover_coord.lda	Functionality for linear discriminant analysis ('lda') objects
recover_coord.lda_ord	Functionality for linear discriminant analysis ('lda') objects
recover_coord.lm	Functionality for linear model objects
recover_coord.lra	Functionality for log-ratio analysis ('lra') objects
recover_coord.mca	Functionality for multiple correspondence analysis ('mca') objects
recover_coord.mlm	Functionality for linear model objects
recover_coord.prcomp	Functionality for principal components analysis ('prcomp') objects
recover_coord.princomp	Functionality for principal components analysis ('princomp') objects
recover_coord.svd_ord	Functionality for singular value decompositions
recover_inertia	Access factors, coordinates, and metadata from ordination objects
recover_inertia.cancor_ord	Functionality for canonical correlations
recover_inertia.cmds_ord	Functionality for classical multidimensional scaling objects
recover_inertia.correspondence	Functionality for correspondence analysis ('correspondence') objects
recover_inertia.default	Access factors, coordinates, and metadata from ordination objects
recover_inertia.eigen	Functionality for eigen-decompositions
recover_inertia.eigen_ord	Functionality for eigen-decompositions
recover_inertia.factanal	Functionality for factor analysis ('factanal') objects
recover_inertia.lda	Functionality for linear discriminant analysis ('lda') objects
recover_inertia.lda_ord	Functionality for linear discriminant analysis ('lda') objects
recover_inertia.lra	Functionality for log-ratio analysis ('lra') objects
recover_inertia.mca	Functionality for multiple correspondence analysis ('mca') objects
recover_inertia.prcomp	Functionality for principal components analysis ('prcomp') objects
recover_inertia.princomp	Functionality for principal components analysis ('princomp') objects
recover_inertia.svd_ord	Functionality for singular value decompositions
recover_rows	Access factors, coordinates, and metadata from ordination objects
recover_rows.cancor_ord	Functionality for canonical correlations
recover_rows.cmds_ord	Functionality for classical multidimensional scaling objects
recover_rows.correspondence	Functionality for correspondence analysis ('correspondence') objects
recover_rows.data.frame	Access factors, coordinates, and metadata from ordination objects
recover_rows.default	Access factors, coordinates, and metadata from ordination objects
recover_rows.eigen	Functionality for eigen-decompositions
recover_rows.eigen_ord	Functionality for eigen-decompositions
recover_rows.factanal	Functionality for factor analysis ('factanal') objects
recover_rows.kmeans	Functionality for k-means clustering ('kmeans') objects
recover_rows.lda	Functionality for linear discriminant analysis ('lda') objects
recover_rows.lda_ord	Functionality for linear discriminant analysis ('lda') objects
recover_rows.lm	Functionality for linear model objects
recover_rows.lra	Functionality for log-ratio analysis ('lra') objects
recover_rows.mca	Functionality for multiple correspondence analysis ('mca') objects
recover_rows.mlm	Functionality for linear model objects
recover_rows.prcomp	Functionality for principal components analysis ('prcomp') objects
recover_rows.princomp	Functionality for principal components analysis ('princomp') objects
recover_rows.svd_ord	Functionality for singular value decompositions
recover_supp_cols	Supplement 'tbl_ord' objects with new data
recover_supp_cols.cancor_ord	Functionality for canonical correlations
recover_supp_cols.default	Supplement 'tbl_ord' objects with new data
recover_supp_rows	Supplement 'tbl_ord' objects with new data
recover_supp_rows.cancor_ord	Functionality for canonical correlations
recover_supp_rows.default	Supplement 'tbl_ord' objects with new data
recover_supp_rows.factanal	Functionality for factor analysis ('factanal') objects
recover_supp_rows.lda	Functionality for linear discriminant analysis ('lda') objects
recover_supp_rows.lda_ord	Functionality for linear discriminant analysis ('lda') objects
recover_supp_rows.mca	Functionality for multiple correspondence analysis ('mca') objects
rename_cols	*dplyr* verbs for tbl_ord factors
rename_rows	*dplyr* verbs for tbl_ord factors
revert_conference	Confer inertia to factors of a 'tbl_ord' object
revert_negation	Negation of ordination axes

-- S --

screeplot.lra	Log-ratio analysis
select_cols	*dplyr* verbs for tbl_ord factors
select_rows	*dplyr* verbs for tbl_ord factors
StatCenter	ggproto classes created and adapted for ordr
StatChull	ggproto classes created and adapted for ordr
StatCols	ggproto classes created and adapted for ordr
StatColsCenter	ggproto classes created and adapted for ordr
StatColsChull	ggproto classes created and adapted for ordr
StatColsCone	ggproto classes created and adapted for ordr
StatColsEllipse	ggproto classes created and adapted for ordr
StatColsScale	ggproto classes created and adapted for ordr
StatColsSpantree	ggproto classes created and adapted for ordr
StatColsStar	ggproto classes created and adapted for ordr
StatCone	ggproto classes created and adapted for ordr
StatRows	ggproto classes created and adapted for ordr
StatRowsCenter	ggproto classes created and adapted for ordr
StatRowsChull	ggproto classes created and adapted for ordr
StatRowsCone	ggproto classes created and adapted for ordr
StatRowsEllipse	ggproto classes created and adapted for ordr
StatRowsScale	ggproto classes created and adapted for ordr
StatRowsSpantree	ggproto classes created and adapted for ordr
StatRowsStar	ggproto classes created and adapted for ordr
StatScale	ggproto classes created and adapted for ordr
StatSpantree	ggproto classes created and adapted for ordr
StatStar	ggproto classes created and adapted for ordr
stat_center	Compute geometric centers and spreads for ordination factors
stat_chull	Restrict geometric data to boundary points for its convex hull
stat_cols	Render plot elements for one matrix of an ordination
stat_cols_center	Convenience stats for row and column matrix factors
stat_cols_chull	Convenience stats for row and column matrix factors
stat_cols_cone	Convenience stats for row and column matrix factors
stat_cols_ellipse	Convenience stats for row and column matrix factors
stat_cols_scale	Convenience stats for row and column matrix factors
stat_cols_spantree	Convenience stats for row and column matrix factors
stat_cols_star	Convenience stats for row and column matrix factors
stat_cone	Restrict geometric data to boundary points for its conical hull
stat_rows	Render plot elements for one matrix of an ordination
stat_rows_center	Convenience stats for row and column matrix factors
stat_rows_chull	Convenience stats for row and column matrix factors
stat_rows_cone	Convenience stats for row and column matrix factors
stat_rows_ellipse	Convenience stats for row and column matrix factors
stat_rows_scale	Convenience stats for row and column matrix factors
stat_rows_spantree	Convenience stats for row and column matrix factors
stat_rows_star	Convenience stats for row and column matrix factors
stat_scale	Multiply artificial coordinates by a scale factor
stat_spantree	Calculate a minimum spanning tree among cases or variables
stat_star	Compute geometric centers and spreads for ordination factors
supplementation	Supplement 'tbl_ord' objects with new data
svd_ord	Wrappers for lossy ordination methods

-- T --

tbl_ord	A unified ordination object class
theme_biplot	Biplot theme
tidiers	Tidiers for 'tbl_ord' objects
tidy.tbl_ord	Tidiers for 'tbl_ord' objects
transmute_cols	*dplyr* verbs for tbl_ord factors
transmute_rows	*dplyr* verbs for tbl_ord factors

-- U --

un_tbl_ord

A unified ordination object class

-- V --

valid_tbl_ord

A unified ordination object class

-- W --

wrap-ord

Wrappers for lossy ordination methods