Man pages for Momocs
Morphometrics using R
| add_ldk | Adds new landmarks on Out and Opn objects |
| arrange | Arrange rows by variables |
| as_df | Turn Momocs objects into tydy data_frames |
| at_least | Retain groups with at least n shapes |
| babel | Convert (x; y) coordinates to chaincoded coordinates |
| bezier | Calculates Bezier coefficients from a shape |
| bezier_i | Calculates a shape from Bezier coefficients |
| boxplot.OutCoe | Boxplot of morphometric coefficients |
| boxplot.PCA | Boxplot on PCA objects |
| breed | Jitters Coe (and others) objects |
| bridges | Convert between different classes |
| calibrate_deviations | Quantitative calibration, through deviations, for Out and Opn... |
| calibrate_harmonicpower | Quantitative calibration, through harmonic power, for Out and... |
| calibrate_r2 | Quantitative r2 calibration for Opn objects |
| calibrate_reconstructions | Calibrate using reconstructed shapes |
| chop | Split to several objects based on a factor |
| classification_metrics | Calculate classification metrics on a confusion matrix |
| CLUST | 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... |
| coeff_split | Converts a numerical description of harmonic coefficients to... |
| color_palettes | Some color palettes |
| color_transparency | Transparency helpers and palettes |
| combine | Combine several objects |
| complex | Convert complex to/from cartesian coordinates |
| Coo | Coo "super" class |
| 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_tangent | 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_centsize | Calculates centroid size |
| coo_check | Checks shapes |
| coo_chull | Calculates the (recursive) convex hull of a shape |
| coo_circularity | Calculates the Haralick's circularity of a shape |
| coo_close | Closes/uncloses shapes |
| coo_convexity | Calculates the convexity of a shape |
| 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_elongation | Calculates the elongation of a shape |
| coo_extract | Extract coordinates from a shape |
| coo_flip | Flips shapes |
| coo_force2close | Forces shapes to close |
| coo_interpolate | Interpolates coordinates |
| coo_intersect_angle | Nearest intersection between a shape and a segment specified... |
| 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_clockwise | Tests if shapes are (likely) developping clockwise or... |
| 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_plot | Plots a single shape |
| coo_range | 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_sample_prop | Sample a proportion of coordinates (among points) |
| coo_samplerr | Samples coordinates (regular radius) |
| coo_scalars | Calculates all scalar descriptors of shape |
| coo_scale | Scales coordinates |
| coo_shear | 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_template | '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_untiltx | Removes rotation so that the centroid and a given point are... |
| coo_up | Retains coordinates with positive y-coordinates |
| coo_width | Calculates the width of a shape |
| d | A wrapper to calculates euclidean distances between two... |
| data_apodemus | Data: Outline coordinates of Apodemus (wood mouse) mandibles |
| data_bot | Data: Outline coordinates of beer and whisky bottles. |
| data_chaff | Data: Landmark and semilandmark coordinates on cereal glumes |
| data_charring | Data: Outline coordinates from an experimental charring on... |
| data_flower | Data: Measurement of iris flowers |
| data_hearts | Data: Outline coordinates of hand-drawn hearts |
| data_molars | Data: Outline coordinates of 360 molars |
| data_mosquito | Data: Outline coordinates of mosquito wings. |
| data_mouse | Data: Outline coordinates of mouse molars |
| data_nsfishes | Data: Outline coordinates of North Sea fishes |
| data_oak | Data: Configuration of landmarks of oak leaves |
| data_olea | Data: Outline coordinates of olive seeds open outlines. |
| data_shapes | Data: Outline coordinates of various shapes |
| data_trilo | Data: Outline coordinates of cephalic outlines of trilobite |
| data_wings | Data: Landmarks coordinates of mosquito wings |
| def_ldk | Defines new landmarks on Out and Opn objects |
| def_ldk_angle | 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_i | Investe discrete cosinus transform |
| dfourier_shape | Calculates and draws 'dfourier' shapes |
| dissolve | Dissolve Coe objects |
| drawers | grindr drawers for shape plots |
| ed | Calculates euclidean distance between two points. |
| edi | Calculates euclidean intermediate between two points. |
| edm | Calculates euclidean distance every pairs of points in two... |
| edm_nearest | Calculates the shortest euclidean distance found for every... |
| efourier | Elliptical Fourier transform (and its normalization) |
| efourier_i | Inverse elliptical Fourier transform |
| efourier_shape | Calculates and draw 'efourier' shapes. |
| export | Exports Coe objects and shapes |
| fac_dispatcher | Brew and serve fac from Momocs object |
| fgProcrustes | Full Generalized Procrustes alignment between shapes |
| fgsProcrustes | Full Generalized Procrustes alignment between shapes with... |
| filter | Subset based on conditions |
| flip_PCaxes | Flips PCA axes |
| fProcrustes | Full Procrustes alignment between two shapes |
| get_chull_area | 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 |
| harm.contrib | Harmonic contribution to shape |
| harm_pow | Calculates harmonic power given a list from e/t/rfourier |
| img_plot | 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 | 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_equallyspacedradii | Tests if coordinates likely have equally spaced radii |
| KMEANS | KMEANS on PCA objects |
| KMEDOIDS | KMEDOIDS |
| layers | grindr layers for multivariate plots |
| layers_morphospace | Morphospace layers |
| LDA | Linear Discriminant Analysis on Coe objects |
| Ldk | 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 |
| 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 |
| MANOVA | Multivariate analysis of (co)variance on Coe objects |
| MANOVA_PW | Pairwise Multivariate analyses of variance |
| MDS | (Metric) multidimensional scaling |
| measure | Measures shape descriptors |
| Momocs | Momocs |
| morphospace_positions | Calculates nice positions on a plane for drawing shapes |
| mosaic | Plots mosaics of shapes. |
| MSHAPES | Mean shape calculation for Coo, Coe, etc. |
| mutate | Add new variables |
| NMDS | Non metric multidimensional scaling |
| npoly | Calculate natural polynomial fits on open outlines |
| Opn | Builds an Opn object |
| OpnCoe | Builds an OpnCoe object |
| opoly | Calculate orthogonal polynomial fits on open outlines |
| Out | Builds an Out object |
| OutCoe | Builds an OutCoe object |
| palettes | Color palettes |
| panel.Coo | Family picture of shapes |
| papers | grindr papers for shape plots |
| PCA | Principal component analysis on Coe objects |
| PCcontrib | Shape variation along PC axes |
| perm | Permutes and breed Coe (and others) objects |
| pile | Graphical pile of shapes |
| plot_CV | Plots a cross-validation table as an heatmap |
| plot_CV2 | Plots a cross-correlation table |
| plot_devsegments | Draws colored segments from a matrix of coordinates. |
| plot_LDA | LDA plot using grindr layers |
| plot.LDA | Plots Linear Discriminant Analysis |
| plot_MSHAPES | Pairwise comparison of a list of shapes |
| plot_NMDS | NMDS plot unsing grindr layers |
| plot_PCA | PCA plot using grindr layers |
| plot.PCA | Plots Principal Component Analysis |
| plot_silhouette | Silhouette plot |
| plot_table | Plots confusion matrix of sample sizes within $fac |
| poly_i | Calculates shape from a polynomial model |
| pProcrustes | Partial Procrustes alignment between two shapes |
| Ptolemy | Ptolemaic ellipses and illustration of efourier |
| rearrange_ldk | Rearrange, (select and reorder) landmarks to retain |
| reexports | Objects exported from other packages |
| reLDA | "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_i | Inverse radii variation Fourier transform |
| rfourier_shape | Calculates and draw 'rfourier' shapes. |
| rm_asym | 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_uncomplete | Remove shapes with incomplete slices |
| rw_fac | Renames levels on Momocs objects |
| sample_frac | Sample a fraction of shapes |
| sample_n | Sample n shapes |
| scree | How many axes to retain this much of variance or trace ? |
| select | Select columns by name |
| sfourier | Radii variation Fourier transform (equally spaced curvilinear... |
| sfourier_i | Inverse radii variation Fourier transform |
| sfourier_shape | Calculates and draw 'sfourier' shapes. |
| slice | Subset based on positions |
| slidings_scheme | Extracts partitions of sliding coordinates |
| stack.Coo | Family picture of shapes |
| subset | Subsetize various Momocs objects |
| symmetry | Calcuates symmetry indices on OutCoe objects |
| tfourier | 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 |
| tps2d | 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 |
| verify | Validates Coo objects |
| which_out | Identify outliers |
