Morphometrics using R
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Documentation for package ‘Momocs’ version 1.4.1
Help Pages
A B C D E F G H I K L M N O P R S T V W
-- A --
| a2l | Convert between different classes |
| a2m | Convert between different classes |
| add_ldk | Adds new landmarks on Out and Opn objects |
| apodemus | Data: Outline coordinates of Apodemus (wood mouse) mandibles |
| arrange | Arrange rows by variables |
| as_df | Turn Momocs objects into tydy data_frames |
| as_df.Coe | Turn Momocs objects into tydy data_frames |
| as_df.Coo | Turn Momocs objects into tydy data_frames |
| as_df.LDA | Turn Momocs objects into tydy data_frames |
| as_df.PCA | Turn Momocs objects into tydy data_frames |
| as_PCA | Principal component analysis on Coe objects |
| at_least | Retain groups with at least n shapes |
-- B --
| bezier | Calculates Bezier coefficients from a shape |
| bezier_i | Calculates a shape from Bezier coefficients |
| bot | Data: Outline coordinates of beer and whisky bottles. |
| boxplot.Coe | Boxplot of morphometric coefficients |
| boxplot.OutCoe | Boxplot of morphometric coefficients |
| boxplot.PCA | Boxplot on PCA objects |
| breed | Jitters Coe (and others) objects |
| breed.Coe | Jitters Coe (and others) objects |
| breed.default | Jitters Coe (and others) objects |
| bridges | Convert between different classes |
-- C --
| calibrate_deviations | Quantitative calibration, through deviations, for Out and Opn objects |
| calibrate_deviations_dfourier | Quantitative calibration, through deviations, for Out and Opn objects |
| calibrate_deviations_efourier | Quantitative calibration, through deviations, for Out and Opn objects |
| calibrate_deviations_npoly | Quantitative calibration, through deviations, for Out and Opn objects |
| calibrate_deviations_opoly | Quantitative calibration, through deviations, for Out and Opn objects |
| calibrate_deviations_rfourier | Quantitative calibration, through deviations, for Out and Opn objects |
| calibrate_deviations_sfourier | Quantitative calibration, through deviations, for Out and Opn objects |
| calibrate_deviations_tfourier | Quantitative calibration, through deviations, for Out and Opn objects |
| calibrate_harmonicpower | Quantitative calibration, through harmonic power, for Out and Opn objects |
| calibrate_harmonicpower_dfourier | Quantitative calibration, through harmonic power, for Out and Opn objects |
| calibrate_harmonicpower_efourier | Quantitative calibration, through harmonic power, for Out and Opn objects |
| calibrate_harmonicpower_rfourier | Quantitative calibration, through harmonic power, for Out and Opn objects |
| calibrate_harmonicpower_sfourier | Quantitative calibration, through harmonic power, for Out and Opn objects |
| calibrate_harmonicpower_tfourier | Quantitative calibration, through harmonic power, for Out and Opn objects |
| calibrate_r2 | Quantitative r2 calibration for Opn objects |
| calibrate_r2_npoly | Quantitative r2 calibration for Opn objects |
| calibrate_r2_opoly | Quantitative r2 calibration for Opn objects |
| calibrate_reconstructions | Calibrate using reconstructed shapes |
| calibrate_reconstructions_dfourier | Calibrate using reconstructed shapes |
| calibrate_reconstructions_efourier | Calibrate using reconstructed shapes |
| calibrate_reconstructions_npoly | Calibrate using reconstructed shapes |
| calibrate_reconstructions_opoly | Calibrate using reconstructed shapes |
| calibrate_reconstructions_rfourier | Calibrate using reconstructed shapes |
| calibrate_reconstructions_sfourier | Calibrate using reconstructed shapes |
| calibrate_reconstructions_tfourier | Calibrate using reconstructed shapes |
| chaff | Data: Landmark and semilandmark coordinates on cereal glumes |
| charring | Data: Outline coordinates from an experimental charring on cereal grains |
| chc2pix | Convert (x; y) coordinates to chaincoded coordinates |
| chop | Split to several objects based on a factor |
| classification_metrics | Calculate classification metrics on a confusion matrix |
| CLUST | Hierarchical clustering |
| CLUST.Coe | Hierarchical clustering |
| CLUST.default | Hierarchical clustering |
| Coe | Coe "super" class |
| coeff_rearrange | Rearrange a matrix of (typically Fourier) coefficients |
| coeff_sel | Helps to select a given number of harmonics from a numerical vector. |
| coeff_split | Converts a numerical description of harmonic coefficients to a named list. |
| color_palettes | Some color palettes |
| col_alpha | Transparency helpers and palettes |
| col_autumn | Some color palettes |
| col_black | Some color palettes |
| col_bw | Some color palettes |
| col_cold | Some color palettes |
| col_gallus | Some color palettes |
| col_grey | Some color palettes |
| col_heat | Some color palettes |
| col_hot | Some color palettes |
| col_india | Some color palettes |
| col_qual | Some color palettes |
| col_sari | Some color palettes |
| col_solarized | Some color palettes |
| col_spring | Some color palettes |
| col_summer | Some color palettes |
| col_summer2 | Some color palettes |
| col_transp | Transparency helpers and palettes |
| combine | Combine several objects |
| complex | Convert complex to/from cartesian coordinates |
| Coo | Coo "super" class |
| coo2cpx | Convert complex to/from cartesian coordinates |
| coo_align | Aligns coordinates |
| coo_aligncalliper | Aligns shapes along their 'calliper length' |
| coo_alignminradius | Aligns shapes using their shortest radius |
| coo_alignxax | Aligns shapes along the x-axis |
| coo_angle_edges | Calculates the angle of every edge of a shape |
| coo_angle_edges.Coo | Calculates the angle of every edge of a shape |
| coo_angle_edges.default | Calculates the angle of every edge of a shape |
| coo_angle_tangent | Calculates the tangent angle along the perimeter of a shape |
| coo_angle_tangent.Coo | Calculates the tangent angle along the perimeter of a shape |
| coo_angle_tangent.default | Calculates the tangent angle along the perimeter of a shape |
| coo_area | Calculates the area of a shape |
| coo_arrows | Plots (lollipop) differences between two configurations |
| coo_baseline | Register new baselines |
| coo_bookstein | Register Bookstein's coordinates |
| coo_boundingbox | Calculates coordinates of the bounding box |
| coo_calliper | Calculates the calliper length |
| coo_centdist | Returns the distance between everypoints and the centroid |
| coo_center | Centers coordinates |
| coo_centpos | Calculate centroid coordinates |
| coo_centre | Centers coordinates |
| coo_centsize | Calculates centroid size |
| coo_check | Checks shapes |
| coo_chull | Calculates the (recursive) convex hull of a shape |
| coo_chull.Coo | Calculates the (recursive) convex hull of a shape |
| coo_chull.default | Calculates the (recursive) convex hull of a shape |
| coo_chull_onion | Calculates the (recursive) convex hull of a shape |
| coo_chull_onion.Coo | Calculates the (recursive) convex hull of a shape |
| coo_chull_onion.default | Calculates the (recursive) convex hull of a shape |
| coo_circularity | Calculates the Haralick's circularity of a shape |
| coo_circularity.Coo | Calculates the Haralick's circularity of a shape |
| coo_circularity.default | Calculates the Haralick's circularity of a shape |
| coo_circularityharalick | Calculates the Haralick's circularity of a shape |
| coo_circularityharalick.Coo | Calculates the Haralick's circularity of a shape |
| coo_circularityharalick.default | Calculates the Haralick's circularity of a shape |
| coo_circularitynorm | Calculates the Haralick's circularity of a shape |
| coo_circularitynorm.Coo | Calculates the Haralick's circularity of a shape |
| coo_circularitynorm.default | Calculates the Haralick's circularity of a shape |
| coo_close | Closes/uncloses shapes |
| coo_convexity | Calculates the convexity of a shape |
| coo_diffrange | Calculate coordinates range |
| coo_diffrange.Coo | Calculate coordinates range |
| coo_diffrange.default | Calculate coordinates range |
| coo_diffrange.list | Calculate coordinates range |
| coo_down | coo_down Retains coordinates with negative y-coordinates |
| coo_draw | Adds a shape to the current plot |
| coo_draw_rads | Draw radii to the current plot |
| coo_dxy | Calculate abscissa and ordinate on a shape |
| coo_eccentricity | Calculates the eccentricity of a shape |
| coo_eccentricityboundingbox | Calculates the eccentricity of a shape |
| coo_eccentricityboundingbox.Coo | Calculates the eccentricity of a shape |
| coo_eccentricityboundingbox.default | Calculates the eccentricity of a shape |
| coo_eccentricityeigen | Calculates the eccentricity of a shape |
| coo_eccentricityeigen.Coo | Calculates the eccentricity of a shape |
| coo_eccentricityeigen.default | Calculates the eccentricity of a shape |
| coo_elongation | Calculates the elongation of a shape |
| coo_extract | Extract coordinates from a shape |
| coo_flipx | Flips shapes |
| coo_flipy | Flips shapes |
| coo_force2close | Forces shapes to close |
| coo_interpolate | Interpolates coordinates |
| coo_intersect_angle | Nearest intersection between a shape and a segment specified with an angle |
| coo_intersect_direction | Nearest intersection between a shape and a segment specified with an angle |
| coo_intersect_direction.Coo | Nearest intersection between a shape and a segment specified with an angle |
| coo_intersect_direction.default | Nearest intersection between a shape and a segment specified with an angle |
| coo_intersect_segment | Nearest intersection between a shape and a segment |
| coo_is_closed | Test if shapes are closed |
| coo_jitter | Jitters shapes |
| coo_ldk | Defines landmarks interactively |
| coo_left | Retains coordinates with negative x-coordinates |
| coo_length | Calculates the length of a shape |
| coo_likely_anticlockwise | Tests if shapes are (likely) developping clockwise or anticlockwise |
| coo_likely_clockwise | Tests if shapes are (likely) developping clockwise or anticlockwise |
| coo_likely_clockwise.Coo | Tests if shapes are (likely) developping clockwise or anticlockwise |
| coo_likely_clockwise.default | Tests if shapes are (likely) developping clockwise or anticlockwise |
| coo_listpanel | Plots sets of shapes. |
| coo_lolli | Plots (lollipop) differences between two configurations |
| coo_lw | Calculates length and width of a shape |
| coo_nb | Counts coordinates |
| coo_oscillo | Momocs' 'oscilloscope' for Fourier-based approaches |
| coo_perim | Calculates perimeter and variations |
| coo_perim.Coo | Calculates perimeter and variations |
| coo_perim.default | Calculates perimeter and variations |
| coo_perimcum | Calculates perimeter and variations |
| coo_perimcum.Coo | Calculates perimeter and variations |
| coo_perimcum.default | Calculates perimeter and variations |
| coo_perimpts | Calculates perimeter and variations |
| coo_perimpts.Coo | Calculates perimeter and variations |
| coo_perimpts.default | Calculates perimeter and variations |
| coo_plot | Plots a single shape |
| coo_range | Calculate coordinates range |
| coo_range.Coo | Calculate coordinates range |
| coo_range.default | Calculate coordinates range |
| coo_range_enlarge | Calculate coordinates range |
| coo_range_enlarge.Coo | Calculate coordinates range |
| coo_range_enlarge.default | Calculate coordinates range |
| coo_range_enlarge.list | Calculate coordinates range |
| coo_rectangularity | Calculates the rectangularity of a shape |
| coo_rectilinearity | Calculates the rectilinearity of a shape |
| coo_rev | Reverses coordinates |
| coo_right | Retains coordinates with positive x-coordinates |
| coo_rotate | Rotates coordinates |
| coo_rotatecenter | Rotates shapes with a custom center |
| coo_ruban | Plots differences as (colored) segments aka a ruban |
| coo_sample | Sample coordinates (among points) |
| coo_samplerr | Samples coordinates (regular radius) |
| coo_sample_prop | Sample a proportion of coordinates (among points) |
| coo_scalars | Calculates all scalar descriptors of shape |
| coo_scale | Scales coordinates |
| coo_scale.Coo | Scales coordinates |
| coo_scale.default | Scales coordinates |
| coo_scalex | Scales coordinates |
| coo_scalex.Coo | Scales coordinates |
| coo_scalex.default | Scales coordinates |
| coo_scaley | Scales coordinates |
| coo_scaley.Coo | Scales coordinates |
| coo_scaley.default | Scales coordinates |
| coo_shearx | Shears shapes |
| coo_sheary | Shears shapes |
| coo_slice | Slices shapes between successive coordinates |
| coo_slide | Slides coordinates |
| coo_slidedirection | Slides coordinates in a particular direction |
| coo_slidegap | Slides coordinates using the widest gap |
| coo_smooth | Smoothes coordinates |
| coo_smoothcurve | Smoothes coordinates on curves |
| coo_solidity | Calculates the solidity of a shape |
| coo_tac | Calculates the total absolute curvature of a shape |
| coo_tangle | Calculates the tangent angle along the perimeter of a shape |
| coo_template | 'Templates' shapes |
| coo_template.Coo | 'Templates' shapes |
| coo_template.default | 'Templates' shapes |
| coo_template.list | 'Templates' shapes |
| coo_template_relatively | 'Templates' shapes |
| coo_template_relatively.Coo | 'Templates' shapes |
| coo_template_relatively.list | 'Templates' shapes |
| coo_trans | Translates coordinates |
| coo_trim | Trims both ends coordinates from shape |
| coo_trimbottom | Trims bottom coordinates from shape |
| coo_trimtop | Trims top coordinates from shape |
| coo_truss | Truss measurement |
| coo_unclose | Closes/uncloses shapes |
| coo_untilt | Removes rotation so that the centroid and a given point are parallel to the x-axis |
| coo_untiltx | Removes rotation so that the centroid and a given point are parallel to the x-axis |
| coo_up | Retains coordinates with positive y-coordinates |
| coo_width | Calculates the width of a shape |
| cpx2coo | Convert complex to/from cartesian coordinates |
-- D --
| d | A wrapper to calculates euclidean distances between two points |
| d2m | Convert between different classes |
| def_ldk | Defines new landmarks on Out and Opn objects |
| def_ldk_angle | Add new landmarks based on angular positions |
| def_ldk_direction | Add new landmarks based on angular positions |
| def_ldk_direction.default | Add new landmarks based on angular positions |
| def_ldk_direction.Opn | Add new landmarks based on angular positions |
| def_ldk_direction.Out | Add new landmarks based on angular positions |
| def_ldk_tips | Define tips as new landmarks |
| def_links | Defines links between landmarks |
| def_slidings | Defines sliding landmarks matrix |
| dfourier | Discrete cosinus transform |
| dfourier.Coo | Discrete cosinus transform |
| dfourier.default | Discrete cosinus transform |
| dfourier.list | Discrete cosinus transform |
| dfourier.Opn | Discrete cosinus transform |
| dfourier_i | Investe discrete cosinus transform |
| dfourier_shape | Calculates and draws 'dfourier' shapes |
| dissolve | Dissolve Coe objects |
| drawers | grindr drawers for shape plots |
| draw_axes | grindr drawers for shape plots |
| draw_centroid | grindr drawers for shape plots |
| draw_curve | grindr drawers for shape plots |
| draw_curves | grindr drawers for shape plots |
| draw_firstpoint | grindr drawers for shape plots |
| draw_labels | grindr drawers for shape plots |
| draw_landmarks | grindr drawers for shape plots |
| draw_lines | grindr drawers for shape plots |
| draw_links | grindr drawers for shape plots |
| draw_outline | grindr drawers for shape plots |
| draw_outlines | grindr drawers for shape plots |
| draw_points | grindr drawers for shape plots |
| draw_polygon | grindr drawers for shape plots |
| draw_ticks | grindr drawers for shape plots |
| draw_title | grindr drawers for shape plots |
-- E --
| ed | Calculates euclidean distance between two points. |
| edi | Calculates euclidean intermediate between two points. |
| edm | Calculates euclidean distance every pairs of points in two matrices. |
| edm_nearest | Calculates the shortest euclidean distance found for every point of one matrix among those of a second. |
| efourier | Elliptical Fourier transform (and its normalization) |
| efourier.default | Elliptical Fourier transform (and its normalization) |
| efourier.list | Elliptical Fourier transform (and its normalization) |
| efourier.Out | Elliptical Fourier transform (and its normalization) |
| efourier_i | Inverse elliptical Fourier transform |
| efourier_norm | Elliptical Fourier transform (and its normalization) |
| efourier_shape | Calculates and draw 'efourier' shapes. |
| export | Exports Coe objects and shapes |
-- F --
| fac_dispatcher | Brew and serve fac from Momocs object |
| fgProcrustes | Full Generalized Procrustes alignment between shapes |
| fgsProcrustes | Full Generalized Procrustes alignment between shapes with sliding landmarks |
| filter | Subset based on conditions |
| flip_PCaxes | Flips PCA axes |
| flower | Data: Measurement of iris flowers |
| fProcrustes | Full Procrustes alignment between two shapes |
-- G --
| get_chull_area | Calculates convex hull area/volume of PCA scores |
| get_chull_volume | Calculates convex hull area/volume of PCA scores |
| get_ldk | Retrieves landmarks coordinates |
| get_pairs | Get paired individual on a Coe, PCA or LDA objects |
| get_slidings | Extracts sliding landmarks coordinates |
-- H --
| harm_pow | Calculates harmonic power given a list from e/t/rfourier |
| hcontrib | Harmonic contribution to shape |
| hcontrib.OutCoe | Harmonic contribution to shape |
| hearts | Data: Outline coordinates of hand-drawn hearts |
-- I --
| img_plot | Plots a .jpg image |
| img_plot0 | Plots a .jpg image |
| import_Conte | Extract outlines coordinates from an image silhouette |
| import_jpg | Extract outline coordinates from multiple .jpg files |
| import_jpg1 | Extract outline coordinates from a single .jpg file |
| import_StereoMorph_curve | Import files creates by StereoMorph into Momocs |
| import_StereoMorph_curve1 | Import files creates by StereoMorph into Momocs |
| import_StereoMorph_ldk | Import files creates by StereoMorph into Momocs |
| import_StereoMorph_ldk1 | Import files creates by StereoMorph into Momocs |
| import_tps | Import a tps file |
| import_txt | Import coordinates from a .txt file |
| inspect | Graphical inspection of shapes |
| is | Class and component testers |
| is_Coe | Class and component testers |
| is_Coo | Class and component testers |
| is_equallyspacedradii | Tests if coordinates likely have equally spaced radii |
| is_fac | Class and component testers |
| is_LDA | Class and component testers |
| is_Ldk | Class and component testers |
| is_ldk | Class and component testers |
| is_LdkCoe | Class and component testers |
| is_links | Class and component testers |
| is_open | Test if shapes are closed |
| is_Opn | Class and component testers |
| is_OpnCoe | Class and component testers |
| is_Out | Class and component testers |
| is_OutCoe | Class and component testers |
| is_PCA | Class and component testers |
| is_shp | Class and component testers |
| is_slidings | Class and component testers |
| is_TraCoe | Class and component testers |
-- K --
| KMEANS | KMEANS on PCA objects |
| KMEANS.PCA | KMEANS on PCA objects |
| KMEDOIDS | KMEDOIDS |
| KMEDOIDS.Coe | KMEDOIDS |
| KMEDOIDS.default | KMEDOIDS |
| KMEDOIDS.PCA | KMEDOIDS |
-- L --
| l2a | Convert between different classes |
| l2m | Convert between different classes |
| layers | grindr layers for multivariate plots |
| layers_morphospace | Morphospace layers |
| layer_axes | grindr layers for multivariate plots |
| layer_axesnames | grindr layers for multivariate plots |
| layer_axesvar | grindr layers for multivariate plots |
| layer_box | grindr layers for multivariate plots |
| layer_chull | grindr layers for multivariate plots |
| layer_chullfilled | grindr layers for multivariate plots |
| layer_delaunay | grindr layers for multivariate plots |
| layer_density | grindr layers for multivariate plots |
| layer_density_2 | grindr layers for multivariate plots |
| layer_eigen | grindr layers for multivariate plots |
| layer_ellipses | grindr layers for multivariate plots |
| layer_ellipsesaxes | grindr layers for multivariate plots |
| layer_ellipsesfilled | grindr layers for multivariate plots |
| layer_frame | grindr layers for multivariate plots |
| layer_fullframe | grindr layers for multivariate plots |
| layer_grid | grindr layers for multivariate plots |
| layer_histogram_2 | grindr layers for multivariate plots |
| layer_labelgroups | grindr layers for multivariate plots |
| layer_labelpoints | grindr layers for multivariate plots |
| layer_legend | grindr layers for multivariate plots |
| layer_morphospace_LDA | Morphospace layers |
| layer_morphospace_PCA | Morphospace layers |
| layer_points | grindr layers for multivariate plots |
| layer_rug | grindr layers for multivariate plots |
| layer_stars | grindr layers for multivariate plots |
| layer_ticks | grindr layers for multivariate plots |
| layer_title | grindr layers for multivariate plots |
| LDA | Linear Discriminant Analysis on Coe objects |
| LDA.default | Linear Discriminant Analysis on Coe objects |
| LDA.PCA | Linear Discriminant Analysis on Coe objects |
| Ldk | Builds an Ldk object |
| LdkCoe | Builds an Ldk object |
| ldk_check | Checks 'ldk' shapes |
| ldk_chull | Draws convex hulls around landmark positions |
| ldk_confell | Draws confidence ellipses for landmark positions |
| ldk_contour | Draws kernel density contours around landmark |
| ldk_labels | Add landmarks labels |
| ldk_links | Draws links between landmarks |
| ldk_plot | Plots a single shape |
| lf_structure | bind_db.Coe <- bind_db.Coo Extracts structure from filenames |
| links_all | Creates links (all pairwise combinations) between landmarks |
| links_delaunay | Creates links (Delaunay triangulation) between landmarks |
-- M --
| m2a | Convert between different classes |
| m2d | Convert between different classes |
| m2l | Convert between different classes |
| m2ll | Convert between different classes |
| MANOVA | Multivariate analysis of (co)variance on Coe objects |
| MANOVA.OpnCoe | Multivariate analysis of (co)variance on Coe objects |
| MANOVA.OutCoe | Multivariate analysis of (co)variance on Coe objects |
| MANOVA.PCA | Multivariate analysis of (co)variance on Coe objects |
| MANOVA_PW | Pairwise Multivariate analyses of variance |
| MANOVA_PW.PCA | Pairwise Multivariate analyses of variance |
| MDS | (Metric) multidimensional scaling |
| measure | Measures shape descriptors |
| molars | Data: Outline coordinates of 360 molars |
| Momocs | Momocs |
| morphospace_positions | Calculates nice positions on a plane for drawing shapes |
| mosaic | Plots mosaics of shapes. |
| mosaic.Ldk | Plots mosaics of shapes. |
| mosaic.Opn | Plots mosaics of shapes. |
| mosaic.Out | Plots mosaics of shapes. |
| mosaic_engine | Plots mosaics of shapes. |
| mosquito | Data: Outline coordinates of mosquito wings. |
| mouse | Data: Outline coordinates of mouse molars |
| MSHAPES | Mean shape calculation for Coo, Coe, etc. |
| mutate | Add new variables |
-- N --
| NMDS | Non metric multidimensional scaling |
| npoly | Calculate natural polynomial fits on open outlines |
| npoly.default | Calculate natural polynomial fits on open outlines |
| npoly.list | Calculate natural polynomial fits on open outlines |
| npoly.Opn | Calculate natural polynomial fits on open outlines |
| npoly_i | Calculates shape from a polynomial model |
| nsfishes | Data: Outline coordinates of North Sea fishes |
-- O --
| oak | Data: Configuration of landmarks of oak leaves |
| olea | Data: Outline coordinates of olive seeds open outlines. |
| Opn | Builds an Opn object |
| OpnCoe | Builds an OpnCoe object |
| opoly | Calculate orthogonal polynomial fits on open outlines |
| opoly.default | Calculate orthogonal polynomial fits on open outlines |
| opoly.list | Calculate orthogonal polynomial fits on open outlines |
| opoly.Opn | Calculate orthogonal polynomial fits on open outlines |
| opoly_i | Calculates shape from a polynomial model |
| Out | Builds an Out object |
| OutCoe | Builds an OutCoe object |
-- P --
| pal | Color palettes |
| palette | Color palettes |
| Palettes | Some color palettes |
| palettes | Color palettes |
| pal_alpha | Color palettes |
| pal_div | Color palettes |
| pal_div_BrBG | Color palettes |
| pal_div_PiYG | Color palettes |
| pal_div_PRGn | Color palettes |
| pal_div_PuOr | Color palettes |
| pal_div_RdBu | Color palettes |
| pal_div_RdYlBu | Color palettes |
| pal_manual | Color palettes |
| pal_qual | Color palettes |
| pal_qual_Dark2 | Color palettes |
| pal_qual_Paired | Color palettes |
| pal_qual_Set2 | Color palettes |
| pal_qual_solarized | Color palettes |
| pal_seq | Color palettes |
| pal_seq_Blues | Color palettes |
| pal_seq_BuGn | Color palettes |
| pal_seq_BuPu | Color palettes |
| pal_seq_GnBu | Color palettes |
| pal_seq_Greens | Color palettes |
| pal_seq_grey | Color palettes |
| pal_seq_Greys | Color palettes |
| pal_seq_inferno | Color palettes |
| pal_seq_magma | Color palettes |
| pal_seq_Oranges | Color palettes |
| pal_seq_OrRd | Color palettes |
| pal_seq_plasma | Color palettes |
| pal_seq_PuBu | Color palettes |
| pal_seq_PuBuGn | Color palettes |
| pal_seq_PuRd | Color palettes |
| pal_seq_Purples | Color palettes |
| pal_seq_RdPu | Color palettes |
| pal_seq_Reds | Color palettes |
| pal_seq_viridis | Color palettes |
| pal_seq_YlGn | Color palettes |
| pal_seq_YlGnBu | Color palettes |
| pal_seq_YlOrBr | Color palettes |
| pal_seq_YlOrRd | Color palettes |
| panel | Family picture of shapes |
| panel.Coo | Family picture of shapes |
| panel.Ldk | Family picture of shapes |
| panel.Opn | Family picture of shapes |
| panel.Out | Family picture of shapes |
| paper | grindr papers for shape plots |
| papers | grindr papers for shape plots |
| paper_chess | grindr papers for shape plots |
| paper_dots | grindr papers for shape plots |
| paper_grid | grindr papers for shape plots |
| paper_white | grindr papers for shape plots |
| PCA | Principal component analysis on Coe objects |
| PCA.default | Principal component analysis on Coe objects |
| PCA.LdkCoe | Principal component analysis on Coe objects |
| PCA.OpnCoe | Principal component analysis on Coe objects |
| PCA.OutCoe | Principal component analysis on Coe objects |
| PCA.TraCoe | Principal component analysis on Coe objects |
| PCcontrib | Shape variation along PC axes |
| PCcontrib.PCA | Shape variation along PC axes |
| perm | Permutes and breed Coe (and others) objects |
| perm.Coe | Permutes and breed Coe (and others) objects |
| perm.default | Permutes and breed Coe (and others) objects |
| pile | Graphical pile of shapes |
| pile.array | Graphical pile of shapes |
| pile.default | Graphical pile of shapes |
| pile.Ldk | Graphical pile of shapes |
| pile.list | Graphical pile of shapes |
| pile.Opn | Graphical pile of shapes |
| pile.Out | Graphical pile of shapes |
| pix2chc | Convert (x; y) coordinates to chaincoded coordinates |
| plot.LDA | Plots Linear Discriminant Analysis |
| plot.PCA | Plots Principal Component Analysis |
| plot_CV | Plots a cross-validation table as an heatmap |
| plot_CV.default | Plots a cross-validation table as an heatmap |
| plot_CV.LDA | Plots a cross-validation table as an heatmap |
| plot_CV2 | Plots a cross-correlation table |
| plot_CV2.LDA | Plots a cross-correlation table |
| plot_CV2.table | Plots a cross-correlation table |
| plot_devsegments | Draws colored segments from a matrix of coordinates. |
| plot_LDA | LDA plot using grindr layers |
| plot_MDS | NMDS plot unsing grindr layers |
| plot_MSHAPES | Pairwise comparison of a list of shapes |
| plot_NMDS | NMDS plot unsing grindr layers |
| plot_PCA | PCA plot using grindr layers |
| plot_silhouette | Silhouette plot |
| plot_table | Plots confusion matrix of sample sizes within $fac |
| pProcrustes | Partial Procrustes alignment between two shapes |
| Ptolemy | Ptolemaic ellipses and illustration of efourier |
-- R --
| rearrange_ldk | Rearrange, (select and reorder) landmarks to retain |
| reLDA | "Redo" a LDA on new data |
| reLDA.Coe | "Redo" a LDA on new data |
| reLDA.default | "Redo" a LDA on new data |
| reLDA.PCA | "Redo" a LDA on new data |
| rename | Rename columns by name |
| rePCA | "Redo" a PCA on a new Coe |
| rescale | Rescale coordinates from pixels to real length units |
| rfourier | Radii variation Fourier transform (equally spaced radii) |
| rfourier.default | Radii variation Fourier transform (equally spaced radii) |
| rfourier.list | Radii variation Fourier transform (equally spaced radii) |
| rfourier.Out | Radii variation Fourier transform (equally spaced radii) |
| rfourier_i | Inverse radii variation Fourier transform |
| rfourier_shape | Calculates and draw 'rfourier' shapes. |
| rm_asym | Removes asymmetric and symmetric variation on OutCoe objects |
| rm_asym.default | Removes asymmetric and symmetric variation on OutCoe objects |
| rm_asym.OutCoe | Removes asymmetric and symmetric variation on OutCoe objects |
| rm_harm | Removes harmonics from Coe objects |
| rm_missing | Remove shapes with missing data in fac |
| rm_sym | Removes asymmetric and symmetric variation on OutCoe objects |
| rm_sym.default | Removes asymmetric and symmetric variation on OutCoe objects |
| rm_sym.OutCoe | Removes asymmetric and symmetric variation on OutCoe objects |
| rm_uncomplete | Remove shapes with incomplete slices |
| rw_fac | Renames levels on Momocs objects |
-- S --
| sample_frac | Sample a fraction of shapes |
| sample_n | Sample n shapes |
| scree | How many axes to retain this much of variance or trace ? |
| scree.LDA | How many axes to retain this much of variance or trace ? |
| scree.PCA | How many axes to retain this much of variance or trace ? |
| scree_min | How many axes to retain this much of variance or trace ? |
| scree_plot | How many axes to retain this much of variance or trace ? |
| select | Select columns by name |
| sfourier | Radii variation Fourier transform (equally spaced curvilinear abscissa) |
| sfourier.default | Radii variation Fourier transform (equally spaced curvilinear abscissa) |
| sfourier.list | Radii variation Fourier transform (equally spaced curvilinear abscissa) |
| sfourier.Out | Radii variation Fourier transform (equally spaced curvilinear abscissa) |
| sfourier_i | Inverse radii variation Fourier transform |
| sfourier_shape | Calculates and draw 'sfourier' shapes. |
| shapes | Data: Outline coordinates of various shapes |
| slice | Subset based on positions |
| slidings_scheme | Extracts partitions of sliding coordinates |
| stack | Family picture of shapes |
| stack.Coo | Family picture of shapes |
| stack.Ldk | Family picture of shapes |
| subsetize | Subsetize various Momocs objects |
| symmetry | Calcuates symmetry indices on OutCoe objects |
-- T --
| tfourier | Tangent angle Fourier transform |
| tfourier.default | Tangent angle Fourier transform |
| tfourier.list | Tangent angle Fourier transform |
| tfourier.Out | Tangent angle Fourier transform |
| tfourier_i | Inverse tangent angle Fourier transform |
| tfourier_shape | Calculates and draws 'tfourier' shapes. |
| tie_jpg_txt | Binds .jpg outlines from .txt landmarks taken on them |
| tps2coo | Import a tps file |
| tps2d | Thin Plate Splines for 2D data |
| tps_apply | Thin Plate Splines for 2D data |
| tps_arr | Deformation 'vector field' using Thin Plate Splines |
| tps_grid | Deformation grids using Thin Plate Splines |
| tps_iso | Deformation isolines using Thin Plate Splines. |
| tps_raw | Vanilla Thin Plate Splines |
| TraCoe | Traditional morphometrics class |
| trilo | Data: Outline coordinates of cephalic outlines of trilobite |
-- V --
| verify | Validates Coo objects |
-- W --
| which_out | Identify outliers |
| wings | Data: Landmarks coordinates of mosquito wings |