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:Jason Cory Brunson [aut, cre], Emily Paul [ctb], John Gracey [aut]

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NEWS

# Install 'ordr' in R:
install.packages('ordr', repos = c('https://corybrunson.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/corybrunson/ordr/issues

Datasets:

On CRAN:

biplotdata-visualizationdimension-reductiongeometric-data-analysisgrammar-of-graphicslog-ratio-analysismultivariate-analysismultivariate-statisticsordinationtidymodelstidyverse

7.06 score 20 stars 24 scripts 169 downloads 146 exports 38 dependencies

Last updated 27 days agofrom:6724b0fae4. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-winNOTEOct 10 2024
R-4.5-linuxNOTEOct 10 2024
R-4.4-winNOTEOct 10 2024
R-4.4-macNOTEOct 10 2024
R-4.3-winNOTEOct 10 2024
R-4.3-macNOTEOct 10 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

multidimensional scaling of variables

Rendered fromcmds-variables.rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2022-10-22
Started: 2021-05-23

Ordination in the tidyverse

Rendered fromordr.rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2022-08-13
Started: 2021-05-23

Readme and manuals

Help Manual

Help pageTopics
Annotate factors of 'tbl_ord' objectsannotation
Augment factors and coordinates of 'tbl_ord' objectsaugmentation augment_ord recover_aug_cols recover_aug_coord recover_aug_rows
Convenience geoms for row and column matrix factorsbiplot-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 factorsbiplot-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' objectconference confer_inertia get_conference recover_conference recover_conference.default revert_conference
*dplyr* verbs for tbl_ord factorscbind_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 functionsdraw-key draw_key_crosslines draw_key_crosspoint draw_key_line
Format a tbl_ord for printingformat format.tbl_ord print.tbl_ord
Axes through the origingeom_axis
Isolines (contour lines)geom_isoline
Intervals depicting ranges, usually about center pointsgeom_lineranges geom_pointranges
Marker or unit circle at the origingeom_origin geom_unit_circle
Text radiating outward from the origingeom_text_radiate
Vectors from the origingeom_vector
Biplots following the grammar of graphicsggbiplot ord_aes
Glass composition dataglass
Augmented implementation of linear discriminant analysislda-ord lda_ord lda_ord.data.frame lda_ord.default lda_ord.formula lda_ord.matrix predict.lda_ord
Log-ratio analysisbiplot.lra lra lra-ord plot.lra print.lra screeplot.lra
Functionality for canonical correlationsas_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 objectsas_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') objectsas_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-decompositionsas_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') objectsas_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') objectsas_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') objectsas_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 objectsas_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') objectsas_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') objectsas_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') objectsas_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') objectsas_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 decompositionsas_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 axesget_negation negate_ord negate_to_first_orthant negation revert_negation
Fit an ordination model to a data objectordinate ordinate.array ordinate.data.frame ordinate.default ordinate.dist ordinate.table
ggproto classes created and adapted for ordrGeomAxis 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' objectsbiplot.tbl_ord plot.tbl_ord screeplot.tbl_ord
U.S. university rankingsqswur_usa
Access factors, coordinates, and metadata from ordination objectsas.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 factorsstat_center stat_star
Restrict geometric data to boundary points for its convex hullstat_chull
Restrict geometric data to boundary points for its conical hullstat_cone
Render plot elements for one matrix of an ordinationstat_cols stat_rows
Multiply artificial coordinates by a scale factorstat_scale
Calculate a minimum spanning tree among cases or variablesstat_spantree
Supplement 'tbl_ord' objects with new datarecover_supp_cols recover_supp_cols.default recover_supp_rows recover_supp_rows.default supplementation
A unified ordination object classas_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 themetheme_biplot
Tidiers for 'tbl_ord' objectsfortify.tbl_ord glance.tbl_ord tidiers tidy.tbl_ord
Wrappers for lossy ordination methodscancor_ord cmdscale_ord eigen_ord svd_ord wrap-ord