A B C D E F G H I K L M N O P R S T V W
| Momocs-package | Momocs |
| a2l | Converts an array of coordinates to a list of matrices |
| a2m | Converts an array of coordinates to a matrix |
| arrange | Arranges (ala dplyr) on Momocs objects |
| as.Out | Convert an OutCoe object into an Out object |
| as.PCA | Principal component analysis on Coe objects |
| as_df | Converts Momocs objects to data.frames |
| at_least | Retains group with at least a certain number of individuals |
| bezier | Calculates Bezier coefficients from a shape |
| bezier_i | Calculates a shape from Bezier coefficients |
| bind_db | Binds with a database |
| 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 |
| calibrate_deviations | Quantitative calibration, through deviations, for Out and Opn objects |
| calibrate_harmonicpower | Quantitative calibration, through harmonic power, for Out and Opn objects |
| calibrate_r2 | Quantitative r2 calibration for Opn objects |
| calibrate_reconstructions | Calibrate using reconstructed shapes |
| chaff | Data: Landmark and semilandmark coordinates on cereal glumes |
| charring | Data: Outline coordinates from an experimental charring on cereal grains |
| chc2Out | Converts chain-coded coordinates to Out object |
| chc2pix | Converts chain-coded coordinates to (x; y) coordinates |
| chop | Chops (rough slicing) Momocs objects |
| classify | Classify using LDA |
| CLUST | Hierarchical clustering |
| CLUST.default | Hierarchical clustering |
| Coe | Coe "super" class |
| 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. |
| 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 | Combines Momocs objects |
| conf_ell | Confidence ellipses |
| 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_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_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 convex hull of a shape |
| coo_circularity | Calculates the circularity of a shape |
| coo_circularityharalick | Calculates the Haralick's circularity of a shape |
| coo_circularitynorm | Calculates the 'normalized' circularity of a shape |
| coo_close | Closes/uncloses shapes |
| coo_compactness | Calculates the circularity of a shape |
| 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_dxy | Calculate abscissa and ordinate on a shape |
| coo_eccentricityboundingbox | Calculates the eccentricity (bounding box) of a shape |
| coo_eccentricityeigen | Calculates the eccentricity (using eigenvalues) 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_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_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 the perimeter |
| coo_perimcum | Calculates the cumulative chordal distance along a shape. |
| coo_perimpts | Calculates the chordal distance along a shape. |
| coo_plot | Plots a single shape |
| coo_plot.default | Plots a single shape |
| 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_scale | Scales coordinates |
| coo_scalex | Shrinks coordinates in one direction |
| coo_scaley | Shrinks coordinates in one direction |
| coo_shapefactor | Calculates the circularity of a shape |
| 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_tangle | Calculates the tangent angle along the perimeter of a shape |
| coo_template | 'Templates' shapes |
| coo_theta3 | Calculate the angle formed by three (x; y) coordinates |
| coo_thetapts | Calculates the angle of every edge of a shape |
| coo_trans | Translates coordinates |
| coo_trim | Trims coordinates from shape |
| coo_unclose | Closes/uncloses shapes |
| 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 points |
| def_ldk | Defines landmarks on Out and Opn objects |
| 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.Opn | Discrete cosinus transform |
| dfourier_i | Investe discrete cosinus transform |
| dfourier_shape | Calculates and draws 'dfourier' shapes |
| dissolve | Dissolves Coe objects |
| 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 |
| efourier.default | Elliptical Fourier transform |
| efourier.Out | Elliptical Fourier transform |
| efourier_i | Inverse elliptical Fourier transform |
| efourier_norm | Normalizes harmonic coefficients. |
| efourier_shape | Calculates and draw 'efourier' shapes. |
| export | Exports Coe objects and shapes |
| fgProcrustes | Full Generalized Procrustes alignment between shapes |
| fgsProcrustes | Full Generalized Procrustes alignment between shapes with sliding landmarks |
| filter | Filters (ala dplyr) on Momocs objects |
| flower | Data: Measurement of iris flowers |
| fProcrustes | Full Procrustes alignment between two shapes |
| 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 |
| 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 |
| hist.Coe | Histogram of morphometric coefficients |
| hist.OutCoe | Histogram of morphometric coefficients |
| img_plot | Plots a .jpg image |
| img_plot0 | Plots a .jpg image |
| import_Conte | Extracts outlines coordinates from an image silhouette |
| import_jpg | Extracts outline coordinates from multiple .jpg files |
| import_jpg1 | Extracts outline coordinates from a single .jpg file |
| import_StereoMorph_curve | Imports files creates by StereoMorph into Momocs |
| import_StereoMorph_curve1 | Imports files creates by StereoMorph into Momocs |
| import_StereoMorph_ldk | Imports files creates by StereoMorph into Momocs |
| import_StereoMorph_ldk1 | Imports files creates by StereoMorph into Momocs |
| import_tps | Imports a tps file |
| import_txt | Imports coordinates from a .txt file |
| is | Various class/component testers |
| is.Coe | Various class/component testers |
| is.Coo | Various class/component testers |
| is.fac | Various class/component testers |
| is.LDA | Various class/component testers |
| is.Ldk | Various class/component testers |
| is.ldk | Various class/component testers |
| is.LdkCoe | Various class/component testers |
| is.links | Various class/component testers |
| is.Opn | Various class/component testers |
| is.OpnCoe | Various class/component testers |
| is.Out | Various class/component testers |
| is.OutCoe | Various class/component testers |
| is.PCA | Various class/component testers |
| is.shp | Various class/component testers |
| is.slidings | Various class/component testers |
| is_closed | Tests if shapes are closed |
| KMEANS | KMEANS on PCA objects |
| KMEANS.PCA | KMEANS on PCA objects |
| l2a | Converts a list of coordinates to an array of coordinates |
| l2m | Converts a list of coordinates to a matrix of coordinates. |
| 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 |
| 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 | Extracts structure from filenames |
| links_all | Creates links (all pariwise combinations) between landmarks |
| links_delaunay | Creates links (Delaunay triangulation) between landmarks |
| m2a | Converts a matrix of coordinates to an array of coordinates |
| m2d | Converts a matrix of coordinates to a data.frame |
| m2l | Converts a matrix of coordinates to a list of coordinates. |
| m2ll | Converts a matrix of coordinates into a list of matrices |
| MANOVA | Multivariate analysis of variance on Coe objects |
| MANOVA.OpnCoe | Multivariate analysis of variance on Coe objects |
| MANOVA.OutCoe | Multivariate analysis of variance on Coe objects |
| MANOVA.PCA | Multivariate analysis of variance on Coe objects |
| MANOVA_PW | Pairwise Multivariate analyses of variance |
| MANOVA_PW.PCA | Pairwise Multivariate analyses of variance |
| measure | Measures shape descriptors |
| molars | Data: Outline coordinates of 360 molars |
| Momocs | Momocs |
| Momocs_help | Browse Momocs online doc |
| Momocs_lastversion | Install and load the last version of Momocs |
| Momocs_version | Get Momocs version |
| mosquito | Data: Outline coordinates of mosquito wings. |
| MSHAPES | Mean shape calculation for Coo, Coe, etc. |
| mshapes | Mean shape calculation for Coo, Coe, etc. |
| mshapes.array | Mean shape calculation for Coo, Coe, etc. |
| mshapes.Ldk | Mean shape calculation for Coo, Coe, etc. |
| mshapes.LdkCoe | Mean shape calculation for Coo, Coe, etc. |
| mshapes.list | Mean shape calculation for Coo, Coe, etc. |
| mshapes.OpnCoe | Mean shape calculation for Coo, Coe, etc. |
| mshapes.OutCoe | Mean shape calculation for Coo, Coe, etc. |
| mshapes.PCA | Mean shape calculation for Coo, Coe, etc. |
| mutate | Mutates (ala dplyr) on Momocs objects |
| nef2Coe | Imports .nef to Coe objects |
| npoly | Calculate natural polynomial fits on open outlines |
| npoly.default | Calculate natural polynomial fits on open outlines |
| npoly.Opn | Calculate natural polynomial fits on open outlines |
| npoly_i | Calculates shape from a polynomial model |
| Ntable | Plots confusion matrix of sample sizes within $fac |
| ntscol2Coo | Imports .nts to Coo objects |
| ntsrow2Coo | Imports .nts to Coo objects |
| 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.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 |
| Palettes | Some 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 |
| panel.OutCoe | Family picture of shapes |
| panel2 | Family picture of shapes (ggplot2) |
| 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 |
| pix2chc | Converts (x; y) coordinates to chaincoded coordinates |
| plot.Coo | Graphical inspection of shapes |
| plot.LDA | Plots Linear Discriminant Analysis |
| plot.PCA | Plots Principal Component Analysis |
| plot2 | Plots Principal Component Analysis ala ggplot2 |
| plot2.PCA | Plots Principal Component Analysis ala ggplot2 |
| plot3 | #' @describeIn plot.PCA #' @export mplot <- plot.PCA Plots a combination of the three first PCs |
| plot3.PCA | #' @describeIn plot.PCA #' @export mplot <- plot.PCA Plots a combination of the three first PCs |
| 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. |
| pos.shapes | Calculates nice positions on a plane for drawing shapes |
| pProcrustes | Partial Procrustes alignment between two shapes |
| Ptolemy | Ptolemaic ellipses and illustration of efourier |
| 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 | Renames (ala dplyr) on Momocs objects |
| rePCA | "Redo" a PCA on a new Coe |
| rescale | Rescale coordinates from pixels to real length units |
| rfourier | Radii variation Fourier transform |
| rfourier.default | Radii variation Fourier transform |
| rfourier.Out | Radii variation Fourier transform |
| 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_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 | Removes shapes with incomplete slices |
| rw_rule | Renames levels on Momocs objects |
| sample_frac | Samples a fraction of shapes in Momocs objects |
| sample_n | Samples n shapes on Momocs objects |
| scree | Methods for PCA eigen values |
| scree.LDA | Methods for PCA eigen values |
| scree.PCA | Methods for PCA eigen values |
| scree_min | Methods for PCA eigen values |
| scree_plot | Methods for PCA eigen values |
| select | Selects (ala dplyr) on Momocs objects |
| shapes | Data: Outline coordinates of various shapes |
| slice | Slices (ala dplyr) on Momocs objects |
| slidings_scheme | Extracts partitions of sliding coordinates |
| stack.Coo | Family picture of shapes |
| stack.Ldk | Family picture of shapes |
| stack2 | Family picture of shapes (ggplot2) |
| subset.Coe | Subsets on Momocs objects |
| subset.Coo | Subsets on Momocs objects |
| subset.PCA | Subsets on Momocs objects |
| symmetry | Calcuates symmetry indices on OutCoe objects |
| table | Cross-tabulates objects |
| table.Coe | Cross-tabulates objects |
| table.Coo | Cross-tabulates objects |
| table.default | Cross-tabulates objects |
| table.LDA | Cross-tabulates objects |
| table.PCA | Cross-tabulates objects |
| tfourier | Tangent angle Fourier transform |
| tfourier.default | 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 | Reads a single tps-like shape as lines |
| 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 |
| transmute | Transmutes (ala dplyr) on Momocs objects |
| trilo | Data: Outline coordinates of cephalic outlines of trilobite |
| truss | Truss measurement |
| validate | Validates Coo objects |
| vecs_param | Some vector utilities. |
| which_out | Remove outliers on Coe |
| wings | Data: Landmarks coordinates of mosquito wings |