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 Momocs: Morphometrics using R
 edm_nearest: Calculates the shortest euclidean distance found for every...
Calculates the shortest euclidean distance found for every point of one matrix among those of a second.
Description
edm_nearest
calculates the shortest euclidean distance found for
every point of one matrix among those of a second. In other words, if
m1, m2
have n
rows, the result will be the shortest distance
for the first point of m1
to any point of m2
and so on,
n
times. This function is used internally but may be of interest for
other analyses.
Usage
1  edm_nearest(m1, m2, full = FALSE)

Arguments
m1 
The first 
m2 
The second 
full 

Details
So far this function is quite time consumming since it performs n \times n euclidean distance computation. If one wishes to align two (or more shapes) Procrustes surimposition may provide a better solution.
Value
If full
is TRUE
, returns a list
with two
components: d
which is for every point of m1
the shortest
distance found between it and any point in m2
, and pos
the
(m2
) row indices of these points. Otherwise returns d
as a
numeric vector of the shortest distances.
See Also
ed, edm, dist.
Examples
1 2 3 
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 a2l: Converts an array of coordinates to a list of matrices
 a2m: Converts an array of coordinates to a matrix
 add_ldk: Adds new landmarks on Out and Opn objects
 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 chaincoded coordinates to Out object
 chc2pix: Converts chaincoded 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 xaxis
 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 ycoordinates
 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 xcoordinates
 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 Fourierbased 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 xcoordinates
 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 both ends coordinates from shape
 coo_trimbottom: Trims bottom coordinates from shape
 coo_trimtop: Trims top coordinates from shape
 coo_up: Retains coordinates with positive ycoordinates
 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 handdrawn 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 new 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 (co)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 crossvalidation table as an heatmap
 plot_CV2: Plots a crosscorrelation 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: Crosstabulates 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 tpslike 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