Extract coordinates from a shape
Extract ids coordinates from a single shape or a Coo object.
It probably only make sense for Coo objects with the same number of coordinates and them being homologous, typically on Ldk.
matrix of (x; y) coordinates, or a Coo object.
Other coo_ utilities:
Other sampling functions:
1 2 3 4 5
- 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_df: Converts Momocs objects to data.frames
- as.Out: Convert an OutCoe object into an Out object
- 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
- boxplot.OutCoe: Boxplot of morphometric coefficients
- boxplot.PCA: Boxplot on PCA objects
- breed: Jitters Coe (and others) objects
- 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
- 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
- Coe: Coe "super" class
- 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
- colors_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_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_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_flip: 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_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_scalexy: Shrinks coordinates in one direction
- 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_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_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_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_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 landmarks on Out and Opn objects
- 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: 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...
- edm_nearest: Calculates the shortest euclidean distance found for every...
- efourier: 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...
- filter: Filters (ala dplyr) on Momocs objects
- 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
- hist.OutCoe: Histogram of morphometric coefficients
- img_plot: 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: 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_closed: Tests if shapes are closed
- KMEANS: 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
- 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: 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_PW: Pairwise Multivariate analyses of variance
- measure: Measures shape descriptors
- Momocs: Momocs
- Momocs_help: Browse Momocs online doc
- Momocs_lastversion: Install and load the last version of Momocs
- Momocs_version: Get Momocs version
- mshapes: 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
- Ntable: Plots confusion matrix of sample sizes within $fac
- ntsrow2Coo: Imports .nts to Coo objects
- 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
- panel2: Family picture of shapes (ggplot2)
- panel.Coo: Family picture of shapes
- PCA: Principal component analysis on Coe objects
- PCcontrib: Shape variation along PC axes
- perm: Permutes and breed Coe (and others) objects
- pix2chc: Converts (x; y) coordinates to chaincoded coordinates
- plot2.PCA: Plots Principal Component Analysis ala ggplot2
- plot3.PCA: #' @describeIn plot.PCA #' @export mplot <- plot.PCA Plots a...
- plot.Coo: Graphical inspection 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: Plots Linear Discriminant Analysis
- plot.PCA: Plots Principal Component Analysis
- poly_i: Calculates shape from a polynomial model
- 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
- reexports: Objects exported from other packages
- reLDA: "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_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_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
- select: Selects (ala dplyr) on Momocs objects
- slice: Slices (ala dplyr) on Momocs objects
- slidings_scheme: Extracts partitions of sliding coordinates
- stack2: Family picture of shapes (ggplot2)
- stack.Coo: Family picture of shapes
- subset: Subsets on Momocs objects
- symmetry: Calcuates symmetry indices on OutCoe objects
- table: Cross-tabulates 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
- tps2coo: Reads a single tps-like shape as lines
- 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
- transmute: Transmutes (ala dplyr) on Momocs objects
- truss: Truss measurement
- validate: Validates Coo objects
- vecs_param: Some vector utilities.
- which_out: Remove outliers on Coe