| Adds new landmarks on Out and Opn objects | add_ldk |
| Data: Outline coordinates of Apodemus (wood mouse) mandibles | apodemus |
| Arrange rows by variables | arrange |
| Turn Momocs objects into tydy data_frames | as_df as_df.Coe as_df.Coo as_df.LDA as_df.PCA |
| Retain groups with at least n shapes | at_least |
| Calculates Bezier coefficients from a shape | bezier |
| Calculates a shape from Bezier coefficients | bezier_i |
| Data: Outline coordinates of beer and whisky bottles. | bot |
| Boxplot of morphometric coefficients | boxplot.Coe boxplot.OutCoe |
| Boxplot on PCA objects | boxplot.PCA |
| Jitters Coe (and others) objects | breed breed.Coe breed.default |
| Convert between different classes | a2l a2m bridges d2m l2a l2m m2a m2d m2l m2ll |
| Quantitative calibration, through deviations, for Out and Opn objects | calibrate_deviations calibrate_deviations_dfourier calibrate_deviations_efourier calibrate_deviations_npoly calibrate_deviations_opoly calibrate_deviations_rfourier calibrate_deviations_sfourier calibrate_deviations_tfourier |
| Quantitative calibration, through harmonic power, for Out and Opn objects | calibrate_harmonicpower calibrate_harmonicpower_dfourier calibrate_harmonicpower_efourier calibrate_harmonicpower_rfourier calibrate_harmonicpower_sfourier calibrate_harmonicpower_tfourier |
| Quantitative r2 calibration for Opn objects | calibrate_r2 calibrate_r2_npoly calibrate_r2_opoly |
| Calibrate using reconstructed shapes | calibrate_reconstructions calibrate_reconstructions_dfourier calibrate_reconstructions_efourier calibrate_reconstructions_npoly calibrate_reconstructions_opoly calibrate_reconstructions_rfourier calibrate_reconstructions_sfourier calibrate_reconstructions_tfourier |
| Data: Landmark and semilandmark coordinates on cereal glumes | chaff |
| Data: Outline coordinates from an experimental charring on cereal grains | charring |
| Split to several objects based on a factor | chop |
| Calculate classification metrics on a confusion matrix | classification_metrics |
| Hierarchical clustering | CLUST CLUST.Coe CLUST.default |
| Coe "super" class | Coe |
| Rearrange a matrix of (typically Fourier) coefficients | coeff_rearrange |
| Helps to select a given number of harmonics from a numerical vector. | coeff_sel |
| Converts a numerical description of harmonic coefficients to a named list. | coeff_split |
| Transparency helpers and palettes | col_alpha col_transp |
| Some color palettes | color_palettes col_autumn col_black col_bw col_cold col_gallus col_grey col_heat col_hot col_india col_qual col_sari col_solarized col_spring col_summer col_summer2 Palettes |
| Combine several objects | combine |
| Convert complex to/from cartesian coordinates | complex coo2cpx cpx2coo |
| Coo "super" class | Coo |
| Aligns coordinates | coo_align |
| Aligns shapes along their 'calliper length' | coo_aligncalliper |
| Aligns shapes using their shortest radius | coo_alignminradius |
| Aligns shapes along the x-axis | coo_alignxax |
| Calculates the angle of every edge of a shape | coo_angle_edges coo_angle_edges.Coo coo_angle_edges.default |
| Calculates the tangent angle along the perimeter of a shape | coo_angle_tangent coo_angle_tangent.Coo coo_angle_tangent.default coo_tangle |
| Calculates the area of a shape | coo_area |
| Plots (lollipop) differences between two configurations | coo_arrows |
| Register new baselines | coo_baseline |
| Register Bookstein's coordinates | coo_bookstein |
| Calculates coordinates of the bounding box | coo_boundingbox |
| Calculates the calliper length | coo_calliper |
| Returns the distance between everypoints and the centroid | coo_centdist |
| Centers coordinates | coo_center coo_centre |
| Calculate centroid coordinates | coo_centpos |
| Calculates centroid size | coo_centsize |
| Checks shapes | coo_check |
| Calculates the (recursive) convex hull of a shape | coo_chull coo_chull.Coo coo_chull.default coo_chull_onion coo_chull_onion.Coo coo_chull_onion.default |
| Calculates the Haralick's circularity of a shape | coo_circularity coo_circularity.Coo coo_circularity.default coo_circularityharalick coo_circularityharalick.Coo coo_circularityharalick.default coo_circularitynorm coo_circularitynorm.Coo coo_circularitynorm.default |
| Closes/uncloses shapes | coo_close coo_unclose |
| Calculates the convexity of a shape | coo_convexity |
| coo_down Retains coordinates with negative y-coordinates | coo_down |
| Adds a shape to the current plot | coo_draw |
| Draw radii to the current plot | coo_draw_rads |
| Calculate abscissa and ordinate on a shape | coo_dxy |
| Calculates the eccentricity of a shape | coo_eccentricity coo_eccentricityboundingbox coo_eccentricityboundingbox.Coo coo_eccentricityboundingbox.default coo_eccentricityeigen coo_eccentricityeigen.Coo coo_eccentricityeigen.default |
| Calculates the elongation of a shape | coo_elongation |
| Extract coordinates from a shape | coo_extract |
| Flips shapes | coo_flipx coo_flipy |
| Forces shapes to close | coo_force2close |
| Interpolates coordinates | coo_interpolate |
| Nearest intersection between a shape and a segment specified with an angle | coo_intersect_angle coo_intersect_direction coo_intersect_direction.Coo coo_intersect_direction.default |
| Nearest intersection between a shape and a segment | coo_intersect_segment |
| Test if shapes are closed | coo_is_closed is_open |
| Jitters shapes | coo_jitter |
| Defines landmarks interactively | coo_ldk |
| Retains coordinates with negative x-coordinates | coo_left |
| Calculates the length of a shape | coo_length |
| Tests if shapes are (likely) developping clockwise or anticlockwise | coo_likely_anticlockwise coo_likely_clockwise coo_likely_clockwise.Coo coo_likely_clockwise.default |
| Plots sets of shapes. | coo_listpanel |
| Plots (lollipop) differences between two configurations | coo_lolli |
| Calculates length and width of a shape | coo_lw |
| Counts coordinates | coo_nb |
| Momocs' 'oscilloscope' for Fourier-based approaches | coo_oscillo |
| Calculates perimeter and variations | coo_perim coo_perim.Coo coo_perim.default coo_perimcum coo_perimcum.Coo coo_perimcum.default coo_perimpts coo_perimpts.Coo coo_perimpts.default |
| Plots a single shape | coo_plot ldk_plot |
| Calculate coordinates range | coo_diffrange coo_diffrange.Coo coo_diffrange.default coo_diffrange.list coo_range coo_range.Coo coo_range.default coo_range_enlarge coo_range_enlarge.Coo coo_range_enlarge.default coo_range_enlarge.list |
| Calculates the rectangularity of a shape | coo_rectangularity |
| Calculates the rectilinearity of a shape | coo_rectilinearity |
| Reverses coordinates | coo_rev |
| Retains coordinates with positive x-coordinates | coo_right |
| Rotates coordinates | coo_rotate |
| Rotates shapes with a custom center | coo_rotatecenter |
| Plots differences as (colored) segments aka a ruban | coo_ruban |
| Sample coordinates (among points) | coo_sample |
| Sample a proportion of coordinates (among points) | coo_sample_prop |
| Samples coordinates (regular radius) | coo_samplerr |
| Calculates all scalar descriptors of shape | coo_scalars |
| Scales coordinates | coo_scale coo_scale.Coo coo_scale.default coo_scalex coo_scalex.Coo coo_scalex.default coo_scaley coo_scaley.Coo coo_scaley.default |
| Shears shapes | coo_shearx coo_sheary |
| Slices shapes between successive coordinates | coo_slice |
| Slides coordinates | coo_slide |
| Slides coordinates in a particular direction | coo_slidedirection |
| Slides coordinates using the widest gap | coo_slidegap |
| Smoothes coordinates | coo_smooth |
| Smoothes coordinates on curves | coo_smoothcurve |
| Calculates the solidity of a shape | coo_solidity |
| Calculates the total absolute curvature of a shape | coo_tac |
| 'Templates' shapes | coo_template coo_template.Coo coo_template.default coo_template.list coo_template_relatively coo_template_relatively.Coo coo_template_relatively.list |
| Translates coordinates | coo_trans |
| Trims both ends coordinates from shape | coo_trim |
| Trims bottom coordinates from shape | coo_trimbottom |
| Trims top coordinates from shape | coo_trimtop |
| Truss measurement | coo_truss |
| Removes rotation so that the centroid and a given point are parallel to the x-axis | coo_untilt coo_untiltx |
| Retains coordinates with positive y-coordinates | coo_up |
| Calculates the width of a shape | coo_width |
| A wrapper to calculates euclidean distances between two points | d |
| Defines new landmarks on Out and Opn objects | def_ldk |
| Add new landmarks based on angular positions | def_ldk_angle def_ldk_direction def_ldk_direction.default def_ldk_direction.Opn def_ldk_direction.Out |
| Define tips as new landmarks | def_ldk_tips |
| Defines links between landmarks | def_links |
| Defines sliding landmarks matrix | def_slidings |
| Discrete cosinus transform | dfourier dfourier.Coo dfourier.default dfourier.list dfourier.Opn |
| Investe discrete cosinus transform | dfourier_i |
| Calculates and draws 'dfourier' shapes | dfourier_shape |
| Dissolve Coe objects | dissolve |
| grindr drawers for shape plots | drawers draw_axes draw_centroid draw_curve draw_curves draw_firstpoint draw_labels draw_landmarks draw_lines draw_links draw_outline draw_outlines draw_points draw_polygon draw_ticks draw_title |
| Calculates euclidean distance between two points. | ed |
| Calculates euclidean intermediate between two points. | edi |
| Calculates euclidean distance every pairs of points in two matrices. | edm |
| Calculates the shortest euclidean distance found for every point of one matrix among those of a second. | edm_nearest |
| Elliptical Fourier transform (and its normalization) | efourier efourier.default efourier.list efourier.Out efourier_norm |
| Inverse elliptical Fourier transform | efourier_i |
| Calculates and draw 'efourier' shapes. | efourier_shape |
| Exports Coe objects and shapes | export |
| Brew and serve fac from Momocs object | fac_dispatcher |
| Full Generalized Procrustes alignment between shapes | fgProcrustes |
| Full Generalized Procrustes alignment between shapes with sliding landmarks | fgsProcrustes |
| Subset based on conditions | filter |
| Flips PCA axes | flip_PCaxes |
| Data: Measurement of iris flowers | flower |
| Full Procrustes alignment between two shapes | fProcrustes |
| Calculates convex hull area/volume of PCA scores | get_chull_area get_chull_volume |
| Retrieves landmarks coordinates | get_ldk |
| Get paired individual on a Coe, PCA or LDA objects | get_pairs |
| Extracts sliding landmarks coordinates | get_slidings |
| Calculates harmonic power given a list from e/t/rfourier | harm_pow |
| Harmonic contribution to shape | hcontrib hcontrib.OutCoe |
| Data: Outline coordinates of hand-drawn hearts | hearts |
| Plots a .jpg image | img_plot img_plot0 |
| Extract outlines coordinates from an image silhouette | import_Conte |
| Extract outline coordinates from multiple .jpg files | import_jpg |
| Extract outline coordinates from a single .jpg file | import_jpg1 |
| Import files creates by StereoMorph into Momocs | import_StereoMorph_curve import_StereoMorph_curve1 import_StereoMorph_ldk import_StereoMorph_ldk1 |
| Import a tps file | import_tps tps2coo |
| Import coordinates from a .txt file | import_txt |
| Graphical inspection of shapes | inspect |
| Class and component testers | is is_Coe is_Coo is_fac is_LDA is_Ldk is_ldk is_LdkCoe is_links is_Opn is_OpnCoe is_Out is_OutCoe is_PCA is_shp is_slidings is_TraCoe |
| Tests if coordinates likely have equally spaced radii | is_equallyspacedradii |
| KMEANS on PCA objects | KMEANS KMEANS.PCA |
| KMEDOIDS | KMEDOIDS KMEDOIDS.Coe KMEDOIDS.default KMEDOIDS.PCA |
| grindr layers for multivariate plots | layers layer_axes layer_axesnames layer_axesvar layer_box layer_chull layer_chullfilled layer_delaunay layer_density layer_density_2 layer_eigen layer_ellipses layer_ellipsesaxes layer_ellipsesfilled layer_frame layer_fullframe layer_grid layer_histogram_2 layer_labelgroups layer_labelpoints layer_legend layer_points layer_rug layer_stars layer_ticks layer_title |
| Morphospace layers | layers_morphospace layer_morphospace_LDA layer_morphospace_PCA |
| Linear Discriminant Analysis on Coe objects | LDA LDA.default LDA.PCA |
| Builds an Ldk object | Ldk LdkCoe |
| Checks 'ldk' shapes | ldk_check |
| Draws convex hulls around landmark positions | ldk_chull |
| Draws confidence ellipses for landmark positions | ldk_confell |
| Draws kernel density contours around landmark | ldk_contour |
| Add landmarks labels | ldk_labels |
| Draws links between landmarks | ldk_links |
| bind_db.Coe <- bind_db.Coo Extracts structure from filenames | lf_structure |
| Creates links (all pairwise combinations) between landmarks | links_all |
| Creates links (Delaunay triangulation) between landmarks | links_delaunay |
| Multivariate analysis of (co)variance on Coe objects | MANOVA MANOVA.OpnCoe MANOVA.OutCoe MANOVA.PCA |
| Pairwise Multivariate analyses of variance | MANOVA_PW MANOVA_PW.PCA |
| (Metric) multidimensional scaling | MDS |
| Measures shape descriptors | measure |
| Data: Outline coordinates of 360 molars | molars |
| Momocs | Momocs |
| Calculates nice positions on a plane for drawing shapes | morphospace_positions |
| Plots mosaics of shapes. | mosaic mosaic.Ldk mosaic.Opn mosaic.Out mosaic_engine |
| Data: Outline coordinates of mosquito wings. | mosquito |
| Data: Outline coordinates of mouse molars | mouse |
| Mean shape calculation for Coo, Coe, etc. | MSHAPES |
| Add new variables | mutate |
| Non metric multidimensional scaling | NMDS |
| Calculate natural polynomial fits on open outlines | npoly npoly.default npoly.list npoly.Opn |
| Data: Outline coordinates of North Sea fishes | nsfishes |
| Data: Configuration of landmarks of oak leaves | oak |
| Data: Outline coordinates of olive seeds open outlines. | olea |
| Builds an Opn object | Opn |
| Builds an OpnCoe object | OpnCoe |
| Calculate orthogonal polynomial fits on open outlines | opoly opoly.default opoly.list opoly.Opn |
| Calculates shape from a polynomial model | npoly_i opoly_i |
| Builds an Out object | Out |
| Builds an OutCoe object | OutCoe |
| Color palettes | pal palette palettes pal_alpha pal_div pal_div_BrBG pal_div_PiYG pal_div_PRGn pal_div_PuOr pal_div_RdBu pal_div_RdYlBu pal_manual pal_qual pal_qual_Dark2 pal_qual_Paired pal_qual_Set2 pal_qual_solarized pal_seq pal_seq_Blues pal_seq_BuGn pal_seq_BuPu pal_seq_GnBu pal_seq_Greens pal_seq_grey pal_seq_Greys pal_seq_inferno pal_seq_magma pal_seq_Oranges pal_seq_OrRd pal_seq_plasma pal_seq_PuBu pal_seq_PuBuGn pal_seq_PuRd pal_seq_Purples pal_seq_RdPu pal_seq_Reds pal_seq_viridis pal_seq_YlGn pal_seq_YlGnBu pal_seq_YlOrBr pal_seq_YlOrRd |
| Family picture of shapes | panel panel.Coo panel.Ldk panel.Opn panel.Out |
| grindr papers for shape plots | paper papers paper_chess paper_dots paper_grid paper_white |
| Principal component analysis on Coe objects | as_PCA PCA PCA.default PCA.LdkCoe PCA.OpnCoe PCA.OutCoe PCA.TraCoe |
| Shape variation along PC axes | PCcontrib PCcontrib.PCA |
| Permutes and breed Coe (and others) objects | perm perm.Coe perm.default |
| Graphical pile of shapes | pile pile.array pile.default pile.Ldk pile.list pile.Opn pile.Out |
| Convert (x; y) coordinates to chaincoded coordinates | chc2pix pix2chc |
| Plots a cross-validation table as an heatmap | plot_CV plot_CV.default plot_CV.LDA |
| Plots a cross-correlation table | plot_CV2 plot_CV2.LDA plot_CV2.table |
| Draws colored segments from a matrix of coordinates. | plot_devsegments |
| LDA plot using grindr layers | plot_LDA |
| Pairwise comparison of a list of shapes | plot_MSHAPES |
| NMDS plot unsing grindr layers | plot_MDS plot_NMDS |
| PCA plot using grindr layers | plot_PCA |
| Silhouette plot | plot_silhouette |
| Plots confusion matrix of sample sizes within $fac | plot_table |
| Plots Linear Discriminant Analysis | plot.LDA |
| Plots Principal Component Analysis | plot.PCA |
| Partial Procrustes alignment between two shapes | pProcrustes |
| Ptolemaic ellipses and illustration of efourier | Ptolemy |
| Rearrange, (select and reorder) landmarks to retain | rearrange_ldk |
| "Redo" a LDA on new data | reLDA reLDA.Coe reLDA.default reLDA.PCA |
| Rename columns by name | rename |
| "Redo" a PCA on a new Coe | rePCA |
| Rescale coordinates from pixels to real length units | rescale |
| Radii variation Fourier transform (equally spaced radii) | rfourier rfourier.default rfourier.list rfourier.Out |
| Inverse radii variation Fourier transform | rfourier_i |
| Calculates and draw 'rfourier' shapes. | rfourier_shape |
| Removes asymmetric and symmetric variation on OutCoe objects | rm_asym rm_asym.default rm_asym.OutCoe rm_sym rm_sym.default rm_sym.OutCoe |
| Removes harmonics from Coe objects | rm_harm |
| Remove shapes with missing data in fac | rm_missing |
| Remove shapes with incomplete slices | rm_uncomplete |
| Renames levels on Momocs objects | rw_fac |
| Sample a fraction of shapes | sample_frac |
| Sample n shapes | sample_n |
| How many axes to retain this much of variance or trace ? | scree scree.LDA scree.PCA scree_min scree_plot |
| Select columns by name | select |
| Radii variation Fourier transform (equally spaced curvilinear abscissa) | sfourier sfourier.default sfourier.list sfourier.Out |
| Inverse radii variation Fourier transform | sfourier_i |
| Calculates and draw 'sfourier' shapes. | sfourier_shape |
| Data: Outline coordinates of various shapes | shapes |
| Subset based on positions | slice |
| Extracts partitions of sliding coordinates | slidings_scheme |
| Family picture of shapes | stack stack.Coo stack.Ldk |
| Subsetize various Momocs objects | subsetize |
| Calcuates symmetry indices on OutCoe objects | symmetry |
| Tangent angle Fourier transform | tfourier tfourier.default tfourier.list tfourier.Out |
| Inverse tangent angle Fourier transform | tfourier_i |
| Calculates and draws 'tfourier' shapes. | tfourier_shape |
| Binds .jpg outlines from .txt landmarks taken on them | tie_jpg_txt |
| Deformation 'vector field' using Thin Plate Splines | tps_arr |
| Deformation grids using Thin Plate Splines | tps_grid |
| Deformation isolines using Thin Plate Splines. | tps_iso |
| Vanilla Thin Plate Splines | tps_raw |
| Thin Plate Splines for 2D data | tps2d tps_apply |
| Traditional morphometrics class | TraCoe |
| Data: Outline coordinates of cephalic outlines of trilobite | trilo |
| Validates Coo objects | verify |
| Identify outliers | which_out |
| Data: Landmarks coordinates of mosquito wings | wings |
