Package: ordr 0.1.1.0001
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/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
biplotdata-visualizationdimension-reductiongeometric-data-analysisgrammar-of-graphicslog-ratio-analysismultivariate-analysismultivariate-statisticsordinationtidymodelstidyverse
Last updated 3 days agofrom:49ef18849c. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win | NOTE | Nov 20 2024 |
| R-4.5-linux | NOTE | Nov 20 2024 |
| R-4.4-win | NOTE | Nov 20 2024 |
| R-4.4-mac | NOTE | Nov 20 2024 |
| R-4.3-win | NOTE | Nov 20 2024 |
| R-4.3-mac | NOTE | Nov 20 2024 |
Exports:%>%as_tbl_ordaugment_ordcancor_ordcbind_colscbind_rowscmdscale_ordconfer_inertiadraw_key_crosslinesdraw_key_crosspointdraw_key_lineeigen_ordgeom_axisgeom_cols_axisgeom_cols_isolinegeom_cols_labelgeom_cols_label_repelgeom_cols_linerangesgeom_cols_pathgeom_cols_pointgeom_cols_pointrangesgeom_cols_polygongeom_cols_textgeom_cols_text_radiategeom_cols_text_repelgeom_cols_vectorgeom_isolinegeom_label_repelgeom_linerangesgeom_origingeom_pointrangesgeom_rows_axisgeom_rows_isolinegeom_rows_labelgeom_rows_label_repelgeom_rows_linerangesgeom_rows_pathgeom_rows_pointgeom_rows_pointrangesgeom_rows_polygongeom_rows_textgeom_rows_text_radiategeom_rows_text_repelgeom_rows_vectorgeom_text_radiategeom_text_repelgeom_unit_circlegeom_vectorGeomAxisGeomIsolineGeomLinerangesGeomOriginGeomPointrangesGeomTextRadiateGeomUnitCircleGeomVectorget_colsget_conferenceget_coordget_inertiaget_negationget_rowsggbiplotglanceis_tbl_ordis.tbl_ordlda_ordleft_join_colsleft_join_rowslramake_tbl_ordmutate_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_centerstat_chullstat_colsstat_cols_centerstat_cols_chullstat_cols_conestat_cols_ellipsestat_cols_scalestat_cols_spantreestat_cols_starstat_conestat_rowsstat_rows_centerstat_rows_chullstat_rows_conestat_rows_ellipsestat_rows_scalestat_rows_spantreestat_rows_starstat_scalestat_spantreestat_starStatCenterStatChullStatColsStatColsCenterStatColsChullStatColsConeStatColsEllipseStatColsScaleStatColsSpantreeStatColsStarStatConeStatRowsStatRowsCenterStatRowsChullStatRowsConeStatRowsEllipseStatRowsScaleStatRowsSpantreeStatRowsStarStatScaleStatSpantreeStatStarsvd_ordtheme_biplottidytransmute_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_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_text geom_cols_text_radiate geom_cols_text_repel geom_cols_vector geom_rows_axis 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_text geom_rows_text_radiate geom_rows_text_repel geom_rows_vector |
| Convenience stats for row and column matrix factors | biplot-stats stat_cols_center stat_cols_chull stat_cols_cone stat_cols_ellipse stat_cols_scale stat_cols_spantree stat_cols_star stat_rows_center stat_rows_chull stat_rows_cone stat_rows_ellipse 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 |
| *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 the origin | geom_axis |
| 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 |
| 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 | GeomAxis GeomIsoline GeomLineranges GeomOrigin GeomPointranges GeomTextRadiate GeomUnitCircle GeomVector ordr-ggproto StatCenter StatChull StatCols StatColsCenter StatColsChull StatColsCone StatColsEllipse StatColsScale StatColsSpantree StatColsStar StatCone StatRows StatRowsCenter StatRowsChull StatRowsCone StatRowsEllipse StatRowsScale StatRowsSpantree StatRowsStar 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 |
| Compute geometric centers and spreads for ordination factors | stat_center stat_star |
| Restrict geometric data to boundary points for its convex hull | stat_chull |
| Restrict geometric data to boundary points for its conical hull | stat_cone |
| Render plot elements for one matrix of an ordination | stat_cols stat_rows |
| 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 |
| Biplot theme | theme_biplot |
| 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 |
