CLUST                   Hierarchical clustering
Coe                     Coe "super" class
Coo                     Coo "super" class
KMEANS                  KMEANS on PCA objects
LDA                     Linear Discriminant Analysis on Coe objects
Ldk                     Builds an Ldk object
MANOVA                  Multivariate analysis of (co)variance on Coe
                        objects
MANOVA_PW               Pairwise Multivariate analyses of variance
Momocs                  Momocs
Momocs_help             Browse Momocs online doc
Momocs_lastversion      Install and load the last version of Momocs
Momocs_version          Get Momocs version
Ntable                  Plots confusion matrix of sample sizes within
                        $fac
Opn                     Builds an Opn object
OpnCoe                  Builds an OpnCoe object
Out                     Builds an Out object
OutCoe                  Builds an OutCoe object
PCA                     Principal component analysis on Coe objects
PCcontrib               Shape variation along PC axes
Ptolemy                 Ptolemaic ellipses and illustration of efourier
TraCoe                  Traditional morphometrics class
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
apodemus                Data: Outline coordinates of Apodemus (wood
                        mouse) mandibles
arrange                 Arranges (ala dplyr) on Momocs objects
as.Out                  Convert an OutCoe object into an Out object
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.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 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
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.
col_summer              Some color palettes
col_transp              Transparency helpers and palettes
combine                 Combines Momocs objects
conf_ell                Confidence ellipses
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_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 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_flipx               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_scalex              Shrinks coordinates in one direction
coo_shearx              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 y-coordinates
coo_width               Calculates the width of a shape
d                       A wrapper to calculates euclidean distances
                        between two points
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 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_i              Inverse elliptical Fourier transform
efourier_norm           Normalizes harmonic coefficients.
efourier_shape          Calculates and draw 'efourier' shapes.
export                  Exports Coe objects and shapes
fProcrustes             Full Procrustes alignment between two 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
flip_PCaxes             Flips PCA axes
flower                  Data: Measurement of iris flowers
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_pow                Calculates harmonic power given a list from
                        e/t/rfourier
hcontrib                Harmonic contribution to shape
hearts                  Data: Outline coordinates of hand-drawn hearts
hist.OutCoe             Histogram of morphometric coefficients
img_plot                Plots a .jpg image
import_Conte            Extracts outlines coordinates from an image
                        silhouette
import_StereoMorph_curve1
                        Imports files creates by StereoMorph into
                        Momocs
import_jpg              Extracts outline coordinates from multiple .jpg
                        files
import_jpg1             Extracts outline coordinates from a single .jpg
                        file
import_tps              Imports a tps file
import_txt              Imports coordinates from a .txt file
is                      Various class/component testers
is_clockwise            Tests if shapes are developping clockwise or
                        anticlockwise
is_closed               Tests if shapes are closed
is_equallyspacedradii   Tests if coordinates likely have equally spaced
                        radii
l2a                     Converts a list of coordinates to an array of
                        coordinates
l2m                     Converts a list of coordinates to a matrix of
                        coordinates.
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
measure                 Measures shape descriptors
molars                  Data: Outline coordinates of 360 molars
mosquito                Data: Outline coordinates of mosquito wings.
mouse                   Data: Outline coordinates of mouse molars
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
ntsrow2Coo              Imports .nts to Coo objects
oak                     Data: Configuration of landmarks of oak leaves
olea                    Data: Outline coordinates of olive seeds open
                        outlines.
opoly                   Calculate orthogonal polynomial fits on open
                        outlines
opoly_i                 Calculates shape from a polynomial model
pProcrustes             Partial Procrustes alignment between two shapes
panel                   Family picture of shapes
panel2                  Family picture of shapes (ggplot2)
perm                    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
plot3                   #' @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_CV2                Plots a cross-correlation table
plot_devsegments        Draws colored segments from a matrix of
                        coordinates.
plot_mshapes            Pairwise comparison of a list of shapes
pos.shapes              Calculates nice positions on a plane for
                        drawing shapes
reLDA                   "Redo" a LDA on new data
rePCA                   "Redo" a PCA on a new Coe
rename                  Renames (ala dplyr) on Momocs objects
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_uncomplete           Removes shapes with incomplete slices
rw_fac                  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
sfourier                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                   Slices (ala dplyr) on Momocs objects
slidings_scheme         Extracts partitions of sliding coordinates
stack.Coo               Family picture of shapes
stack2                  Family picture of shapes (ggplot2)
subset.Coo              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
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               Identify outliers
wings                   Data: Landmarks coordinates of mosquito wings
