A 'Tidyverse' Extension for Ordinations and Biplots


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Documentation for package ‘ordr’ version 0.2.0

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

-- 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
biplot.tbl_ord Plot and biplot methods for 'tbl_ord' objects

-- 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
CoordScaffold ggproto classes created and adapted for ordr
coord_scaffold Convenience coordinate system for scaffolding axes

-- 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 --

GeomInterpolation ggproto classes created and adapted for ordr
GeomOrigin ggproto classes created and adapted for ordr
GeomUnitCircle ggproto classes created and adapted for ordr
geom_cols_axis Convenience geoms for row and column matrix factors
geom_cols_bagplot Convenience geoms for row and column matrix factors
geom_cols_contour Convenience geoms for row and column matrix factors
geom_cols_density_2d Convenience geoms for row and column matrix factors
geom_cols_density_2d_filled Convenience geoms for row and column matrix factors
geom_cols_interpolation 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_rule 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_interpolation Render interpolation of new rows from columns (or vice-versa)
geom_origin Marker or unit circle at the origin
geom_rows_axis Convenience geoms for row and column matrix factors
geom_rows_bagplot Convenience geoms for row and column matrix factors
geom_rows_contour Convenience geoms for row and column matrix factors
geom_rows_density_2d Convenience geoms for row and column matrix factors
geom_rows_density_2d_filled Convenience geoms for row and column matrix factors
geom_rows_interpolation 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_rule 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_unit_circle Marker or unit circle at 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-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
recover_supp_rows.princomp Functionality for principal components analysis ('princomp') 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
screeplot.tbl_ord Plot and biplot methods for 'tbl_ord' objects
select_cols *dplyr* verbs for tbl_ord factors
select_rows *dplyr* verbs for tbl_ord factors
StatCols ggproto classes created and adapted for ordr
StatColsBagplot 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
StatColsDensity2d ggproto classes created and adapted for ordr
StatColsDensity2dFilled ggproto classes created and adapted for ordr
StatColsDepth ggproto classes created and adapted for ordr
StatColsDepthFilled ggproto classes created and adapted for ordr
StatColsEllipse ggproto classes created and adapted for ordr
StatColsPeel ggproto classes created and adapted for ordr
StatColsProjection ggproto classes created and adapted for ordr
StatColsRule 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
StatProjection ggproto classes created and adapted for ordr
StatRows ggproto classes created and adapted for ordr
StatRowsBagplot 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
StatRowsDensity2d ggproto classes created and adapted for ordr
StatRowsDensity2dFilled ggproto classes created and adapted for ordr
StatRowsDepth ggproto classes created and adapted for ordr
StatRowsDepthFilled ggproto classes created and adapted for ordr
StatRowsEllipse ggproto classes created and adapted for ordr
StatRowsPeel ggproto classes created and adapted for ordr
StatRowsProjection ggproto classes created and adapted for ordr
StatRowsRule 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
stat_cols Render plot elements for one matrix of an ordination
stat_cols_bagplot Convenience stats for row and column matrix factors
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_density_2d Convenience stats for row and column matrix factors
stat_cols_density_2d_filled Convenience stats for row and column matrix factors
stat_cols_depth Convenience stats for row and column matrix factors
stat_cols_depth_filled Convenience stats for row and column matrix factors
stat_cols_ellipse Convenience stats for row and column matrix factors
stat_cols_peel Convenience stats for row and column matrix factors
stat_cols_projection Convenience stats for row and column matrix factors
stat_cols_rule 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_projection Project rows onto columns or vice-versa
stat_rows Render plot elements for one matrix of an ordination
stat_rows_bagplot Convenience stats for row and column matrix factors
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_density_2d Convenience stats for row and column matrix factors
stat_rows_density_2d_filled Convenience stats for row and column matrix factors
stat_rows_depth Convenience stats for row and column matrix factors
stat_rows_depth_filled Convenience stats for row and column matrix factors
stat_rows_ellipse Convenience stats for row and column matrix factors
stat_rows_peel Convenience stats for row and column matrix factors
stat_rows_projection Convenience stats for row and column matrix factors
stat_rows_rule 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
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 Scaffolding theme
theme_scaffold Scaffolding 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