Package: ordr 0.1.1.0002
ordr: A Tidyverse Extension for Ordinations and Biplots
Ordination comprises several multivariate exploratory and explanatory techniques with theoretical foundations in geometric data analysis; see Podani (2000, ISBN:90-5782-067-6) for techniques and applications and Le Roux & Rouanet (2005) <doi:10.1007/1-4020-2236-0> for foundations. Greenacre (2010, ISBN:978-84-923846) shows how the most established of these, including principal components analysis, correspondence analysis, multidimensional scaling, factor analysis, and discriminant analysis, rely on eigen-decompositions or singular value decompositions of pre-processed numeric matrix data. These decompositions give rise to a set of shared coordinates along which the row and column elements can be measured. The overlay of their scatterplots on these axes, introduced by Gabriel (1971) <doi:10.1093/biomet/58.3.453>, is called a biplot. 'ordr' provides inspection, extraction, manipulation, and visualization tools for several popular ordination classes supported by a set of recovery methods. It is inspired by and designed to integrate into 'tidyverse' workflows provided by Wickham et al (2019) <doi:10.21105/joss.01686>.
Authors:
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ordr.pdf |ordr.html✨
ordr/json (API)
NEWS
| # Install 'ordr' in R: |
| install.packages('ordr', repos = c('https://corybrunson.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/corybrunson/ordr/issues
Pkgdown site:https://corybrunson.github.io
biplotdata-visualizationdimension-reductiongeometric-data-analysisgrammar-of-graphicslog-ratio-analysismultivariate-analysismultivariate-statisticsordinationtidymodelstidyverse
Last updated 2 days agofrom:5ed1a782bb. Checks:1 OK, 7 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 16 2025 |
| R-4.5-win | NOTE | Feb 16 2025 |
| R-4.5-mac | NOTE | Feb 16 2025 |
| R-4.5-linux | NOTE | Feb 16 2025 |
| R-4.4-win | NOTE | Feb 16 2025 |
| R-4.4-mac | NOTE | Feb 16 2025 |
| R-4.3-win | NOTE | Feb 16 2025 |
| R-4.3-mac | NOTE | Feb 16 2025 |
Exports:%>%as_tbl_ordaugment_ordcancor_ordcbind_colscbind_rowscmdscale_ordconfer_inertiacoord_rectcoord_scaffoldcoord_squareCoordRectCoordScaffolddraw_key_crosslinesdraw_key_crosspointdraw_key_lineeigen_ordgeom_axisgeom_bagplotgeom_cols_axisgeom_cols_bagplotgeom_cols_contourgeom_cols_density_2dgeom_cols_density_2d_filledgeom_cols_interpolationgeom_cols_isolinegeom_cols_labelgeom_cols_label_repelgeom_cols_linerangesgeom_cols_pathgeom_cols_pointgeom_cols_pointrangesgeom_cols_polygongeom_cols_rulegeom_cols_textgeom_cols_text_radiategeom_cols_text_repelgeom_cols_vectorgeom_interpolationgeom_isolinegeom_label_repelgeom_linerangesgeom_origingeom_pointrangesgeom_rows_axisgeom_rows_bagplotgeom_rows_contourgeom_rows_density_2dgeom_rows_density_2d_filledgeom_rows_interpolationgeom_rows_isolinegeom_rows_labelgeom_rows_label_repelgeom_rows_linerangesgeom_rows_pathgeom_rows_pointgeom_rows_pointrangesgeom_rows_polygongeom_rows_rulegeom_rows_textgeom_rows_text_radiategeom_rows_text_repelgeom_rows_vectorgeom_rulegeom_text_radiategeom_text_repelgeom_unit_circlegeom_vectorGeomAxisGeomBagplotGeomInterpolationGeomIsolineGeomLinerangesGeomOriginGeomPointrangesGeomRuleGeomTextRadiateGeomUnitCircleGeomVectorget_colsget_conferenceget_coordget_inertiaget_negationget_rowsggbiplotglanceis_tbl_ordis.syncis.tbl_ordlda_ordleft_join_colsleft_join_rowslramake_tbl_ordmaxppminabsppminppmutate_colsmutate_rowsnegate_ordnegate_to_first_orthantord_aesordinatepull_colspull_rowsrecover_aug_colsrecover_aug_coordrecover_aug_rowsrecover_colsrecover_conferencerecover_coordrecover_inertiarecover_rowsrecover_supp_colsrecover_supp_rowsrename_colsrename_rowsrevert_conferencerevert_negationselect_colsselect_rowsstat_bagplotstat_centerstat_chullstat_colsstat_cols_bagplotstat_cols_centerstat_cols_chullstat_cols_conestat_cols_density_2dstat_cols_density_2d_filledstat_cols_depthstat_cols_depth_filledstat_cols_ellipsestat_cols_peelstat_cols_projectionstat_cols_rulestat_cols_scalestat_cols_spantreestat_cols_starstat_conestat_depthstat_depth_filledstat_peelstat_projectionstat_referentstat_rowsstat_rows_bagplotstat_rows_centerstat_rows_chullstat_rows_conestat_rows_density_2dstat_rows_density_2d_filledstat_rows_depthstat_rows_depth_filledstat_rows_ellipsestat_rows_peelstat_rows_projectionstat_rows_rulestat_rows_scalestat_rows_spantreestat_rows_starstat_rulestat_scalestat_spantreestat_starStatBagplotStatCenterStatChullStatColsStatColsBagplotStatColsCenterStatColsChullStatColsConeStatColsDensity2dStatColsDensity2dFilledStatColsDepthStatColsDepthFilledStatColsEllipseStatColsPeelStatColsProjectionStatColsRuleStatColsScaleStatColsSpantreeStatColsStarStatConeStatDepthStatDepthFilledStatPeelStatProjectionStatReferentStatRowsStatRowsBagplotStatRowsCenterStatRowsChullStatRowsConeStatRowsDensity2dStatRowsDensity2dFilledStatRowsDepthStatRowsDepthFilledStatRowsEllipseStatRowsPeelStatRowsProjectionStatRowsRuleStatRowsScaleStatRowsSpantreeStatRowsStarStatRuleStatScaleStatSpantreeStatStarsvd_ordsynctheme_biplottheme_scaffoldtidytransmute_colstransmute_rowsun_tbl_ordvalid_tbl_ord
Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggplot2ggrepelgluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate factors of 'tbl_ord' objects | annotation |
| Augment factors and coordinates of 'tbl_ord' objects | augmentation augment_ord recover_aug_cols recover_aug_coord recover_aug_rows |
| Convenience geoms for row and column matrix factors | biplot-geoms geom_cols_axis geom_cols_bagplot geom_cols_contour geom_cols_density_2d geom_cols_density_2d_filled geom_cols_interpolation geom_cols_isoline geom_cols_label geom_cols_label_repel geom_cols_lineranges geom_cols_path geom_cols_point geom_cols_pointranges geom_cols_polygon geom_cols_rule geom_cols_text geom_cols_text_radiate geom_cols_text_repel geom_cols_vector geom_rows_axis geom_rows_bagplot geom_rows_contour geom_rows_density_2d geom_rows_density_2d_filled geom_rows_interpolation geom_rows_isoline geom_rows_label geom_rows_label_repel geom_rows_lineranges geom_rows_path geom_rows_point geom_rows_pointranges geom_rows_polygon geom_rows_rule geom_rows_text geom_rows_text_radiate geom_rows_text_repel geom_rows_vector |
| Convenience stats for row and column matrix factors | biplot-stats stat_cols_bagplot stat_cols_center stat_cols_chull stat_cols_cone stat_cols_density_2d stat_cols_density_2d_filled stat_cols_depth stat_cols_depth_filled stat_cols_ellipse stat_cols_peel stat_cols_projection stat_cols_rule stat_cols_scale stat_cols_spantree stat_cols_star stat_rows_bagplot stat_rows_center stat_rows_chull stat_rows_cone stat_rows_density_2d stat_rows_density_2d_filled stat_rows_depth stat_rows_depth_filled stat_rows_ellipse stat_rows_peel stat_rows_projection stat_rows_rule stat_rows_scale stat_rows_spantree stat_rows_star |
| Confer inertia to factors of a 'tbl_ord' object | conference confer_inertia get_conference recover_conference recover_conference.default revert_conference |
| Cartesian coordinates and plotting window with fixed aspect ratios | coord_rect coord_square |
| Convenience coordinate system for scaffolding axes | coord_scaffold |
| *dplyr* verbs for tbl_ord factors | cbind_cols cbind_rows dplyr-verbs left_join_cols left_join_rows mutate_cols mutate_rows pull_cols pull_factor pull_rows rename_cols rename_rows select_cols select_rows transmute_cols transmute_rows |
| Biplot key drawing functions | draw-key draw_key_crosslines draw_key_crosspoint draw_key_line |
| Format a tbl_ord for printing | format format.tbl_ord print.tbl_ord |
| Axes through or offset from the origin | geom_axis |
| Bagplots | geom_bagplot |
| Render interpolation of new rows from columns (or vice-versa) | geom_interpolation |
| Isolines (contour lines) | geom_isoline |
| Intervals depicting ranges, usually about center points | geom_lineranges geom_pointranges |
| Marker or unit circle at the origin | geom_origin geom_unit_circle |
| Rulers through or offset from the origin | geom_rule |
| Text radiating outward from the origin | geom_text_radiate |
| Vectors from the origin | geom_vector |
| Biplots following the grammar of graphics | ggbiplot ord_aes |
| Glass composition data | glass |
| Augmented implementation of linear discriminant analysis | lda-ord lda_ord lda_ord.data.frame lda_ord.default lda_ord.formula lda_ord.matrix predict.lda_ord |
| Log-ratio analysis | biplot.lra lra lra-ord plot.lra print.lra screeplot.lra |
| Functionality for canonical correlations | as_tbl_ord.cancor_ord methods-cancor recover_aug_cols.cancor_ord recover_aug_coord.cancor_ord recover_aug_rows.cancor_ord recover_cols.cancor_ord recover_conference.cancor_ord recover_coord.cancor_ord recover_inertia.cancor_ord recover_rows.cancor_ord recover_supp_cols.cancor_ord recover_supp_rows.cancor_ord |
| Functionality for classical multidimensional scaling objects | as_tbl_ord.cmds_ord methods-cmds recover_aug_cols.cmds_ord recover_aug_coord.cmds_ord recover_aug_rows.cmds_ord recover_cols.cmds_ord recover_conference.cmds_ord recover_coord.cmds_ord recover_inertia.cmds_ord recover_rows.cmds_ord |
| Functionality for correspondence analysis ('correspondence') objects | as_tbl_ord.correspondence methods-correspondence recover_aug_cols.correspondence recover_aug_coord.correspondence recover_aug_rows.correspondence recover_cols.correspondence recover_conference.correspondence recover_coord.correspondence recover_inertia.correspondence recover_rows.correspondence |
| Functionality for eigen-decompositions | as_tbl_ord.eigen as_tbl_ord.eigen_ord methods-eigen recover_aug_cols.eigen_ord recover_aug_coord.eigen recover_aug_coord.eigen_ord recover_aug_rows.eigen_ord recover_cols.eigen recover_cols.eigen_ord recover_conference.eigen recover_conference.eigen_ord recover_coord.eigen recover_coord.eigen_ord recover_inertia.eigen recover_inertia.eigen_ord recover_rows.eigen recover_rows.eigen_ord |
| Functionality for factor analysis ('factanal') objects | as_tbl_ord.factanal methods-factanal recover_aug_cols.factanal recover_aug_coord.factanal recover_aug_rows.factanal recover_cols.factanal recover_conference.factanal recover_coord.factanal recover_inertia.factanal recover_rows.factanal recover_supp_rows.factanal |
| Functionality for k-means clustering ('kmeans') objects | as_tbl_ord.kmeans methods-kmeans recover_aug_cols.kmeans recover_aug_coord.kmeans recover_aug_rows.kmeans recover_cols.kmeans recover_coord.kmeans recover_rows.kmeans |
| Functionality for linear discriminant analysis ('lda') objects | as_tbl_ord.lda as_tbl_ord.lda_ord methods-lda recover_aug_cols.lda recover_aug_cols.lda_ord recover_aug_coord.lda recover_aug_coord.lda_ord recover_aug_rows.lda recover_aug_rows.lda_ord recover_cols.lda recover_cols.lda_ord recover_conference.lda recover_conference.lda_ord recover_coord.lda recover_coord.lda_ord recover_inertia.lda recover_inertia.lda_ord recover_rows.lda recover_rows.lda_ord recover_supp_rows.lda recover_supp_rows.lda_ord |
| Functionality for linear model objects | as_tbl_ord.lm methods-lm recover_aug_cols.lm recover_aug_cols.mlm recover_aug_coord.lm recover_aug_coord.mlm recover_aug_rows.glm recover_aug_rows.lm recover_aug_rows.mlm recover_cols.lm recover_cols.mlm recover_coord.lm recover_coord.mlm recover_rows.lm recover_rows.mlm |
| Functionality for log-ratio analysis ('lra') objects | as_tbl_ord.lra methods-lra recover_aug_cols.lra recover_aug_coord.lra recover_aug_rows.lra recover_cols.lra recover_conference.lra recover_coord.lra recover_inertia.lra recover_rows.lra |
| Functionality for multiple correspondence analysis ('mca') objects | as_tbl_ord.mca methods-mca recover_aug_cols.mca recover_aug_coord.mca recover_aug_rows.mca recover_cols.mca recover_conference.mca recover_coord.mca recover_inertia.mca recover_rows.mca recover_supp_rows.mca |
| Functionality for principal components analysis ('prcomp') objects | as_tbl_ord.prcomp methods-prcomp recover_aug_cols.prcomp recover_aug_coord.prcomp recover_aug_rows.prcomp recover_cols.prcomp recover_conference.prcomp recover_coord.prcomp recover_inertia.prcomp recover_rows.prcomp |
| Functionality for principal components analysis ('princomp') objects | as_tbl_ord.princomp methods-princomp recover_aug_cols.princomp recover_aug_coord.princomp recover_aug_rows.princomp recover_cols.princomp recover_conference.princomp recover_coord.princomp recover_inertia.princomp recover_rows.princomp recover_supp_rows.princomp |
| Functionality for singular value decompositions | as_tbl_ord.svd_ord methods-svd recover_aug_cols.svd_ord recover_aug_coord.svd_ord recover_aug_rows.svd_ord recover_cols.svd_ord recover_conference.svd_ord recover_coord.svd_ord recover_inertia.svd_ord recover_rows.svd_ord |
| Negation of ordination axes | get_negation negate_ord negate_to_first_orthant negation revert_negation |
| Fit an ordination model to a data object | ordinate ordinate.array ordinate.data.frame ordinate.default ordinate.dist ordinate.table |
| ggproto classes created and adapted for ordr | CoordRect CoordScaffold GeomAxis GeomBagplot GeomInterpolation GeomIsoline GeomLineranges GeomOrigin GeomPointranges GeomRule GeomTextRadiate GeomUnitCircle GeomVector ordr-ggproto StatBagplot StatCenter StatChull StatCols StatColsBagplot StatColsCenter StatColsChull StatColsCone StatColsDensity2d StatColsDensity2dFilled StatColsDepth StatColsDepthFilled StatColsEllipse StatColsPeel StatColsProjection StatColsRule StatColsScale StatColsSpantree StatColsStar StatCone StatDepth StatDepthFilled StatPeel StatProjection StatReferent StatRows StatRowsBagplot StatRowsCenter StatRowsChull StatRowsCone StatRowsDensity2d StatRowsDensity2dFilled StatRowsDepth StatRowsDepthFilled StatRowsEllipse StatRowsPeel StatRowsProjection StatRowsRule StatRowsScale StatRowsSpantree StatRowsStar StatRule StatScale StatSpantree StatStar |
| Plot and biplot methods for 'tbl_ord' objects | biplot.tbl_ord plot.tbl_ord screeplot.tbl_ord |
| U.S. university rankings | qswur_usa |
| Access factors, coordinates, and metadata from ordination objects | as.matrix.tbl_ord dim.tbl_ord get_cols get_coord get_inertia get_rows recoverers recover_cols recover_cols.data.frame recover_cols.default recover_coord recover_coord.data.frame recover_coord.default recover_inertia recover_inertia.default recover_rows recover_rows.data.frame recover_rows.default |
| Bagplots | stat_bagplot |
| Compute geometric centers and spreads for ordination factors | stat_center stat_star |
| Convex hulls and hull peelings | stat_chull stat_peel |
| Conical hull | stat_cone |
| Depth estimates and contours | stat_depth stat_depth_filled |
| Project rows onto columns or vice-versa | stat_projection |
| Transformations with respect to reference data | ggplot_add.LayerRef stat_referent |
| Render plot elements for one matrix of an ordination | stat_cols stat_rows |
| Construct limited rules offset from the origin | maxpp minabspp minpp stat_rule |
| Multiply artificial coordinates by a scale factor | stat_scale |
| Calculate a minimum spanning tree among cases or variables | stat_spantree |
| Supplement 'tbl_ord' objects with new data | recover_supp_cols recover_supp_cols.default recover_supp_rows recover_supp_rows.default supplementation |
| A unified ordination object class | as_tbl_ord as_tbl_ord.tbl_ord is.tbl_ord is_tbl_ord make_tbl_ord tbl_ord un_tbl_ord valid_tbl_ord |
| Scaffolding theme | theme_biplot theme_scaffold |
| Tidiers for 'tbl_ord' objects | fortify.tbl_ord glance.tbl_ord tidiers tidy.tbl_ord |
| Wrappers for lossy ordination methods | cancor_ord cmdscale_ord eigen_ord svd_ord wrap-ord |
