# A 'tidyverse' Extension for Ordinations and Biplots

## Documentation for package ‘ordr’ version 0.1.2

- 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
model.frame.lda_ord | Augmented implementation of linear discriminant analysis
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