# Morphometrics using R

## Documentation for package ‘Momocs’ version 1.3.0

- DESCRIPTION file.

## Help Pages

A B C D E F G H I K L M N O P R S T V W

## -- A --

a2l | Convert between different classes
a2m | Convert between different classes
add_ldk | Adds new landmarks on Out and Opn objects
apodemus | Data: Outline coordinates of Apodemus (wood mouse) mandibles
arrange | Arrange rows by variables
as_df | Turn Momocs objects into tydy data_frames
as_df.Coe | Turn Momocs objects into tydy data_frames
as_df.Coo | Turn Momocs objects into tydy data_frames
as_df.LDA | Turn Momocs objects into tydy data_frames
as_df.PCA | Turn Momocs objects into tydy data_frames
as_PCA | Principal component analysis on Coe objects
at_least | Retain groups with at least n shapes

## -- B --

bezier | Calculates Bezier coefficients from a shape
bezier_i | Calculates a shape from Bezier coefficients
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
bridges | Convert between different classes

## -- C --

calibrate_deviations | Quantitative calibration, through deviations, for Out and Opn objects
calibrate_deviations_dfourier | Quantitative calibration, through deviations, for Out and Opn objects
calibrate_deviations_efourier | Quantitative calibration, through deviations, for Out and Opn objects
calibrate_deviations_npoly | Quantitative calibration, through deviations, for Out and Opn objects
calibrate_deviations_opoly | Quantitative calibration, through deviations, for Out and Opn objects
calibrate_deviations_rfourier | Quantitative calibration, through deviations, for Out and Opn objects
calibrate_deviations_sfourier | Quantitative calibration, through deviations, for Out and Opn objects
calibrate_deviations_tfourier | Quantitative calibration, through deviations, for Out and Opn objects
calibrate_harmonicpower | Quantitative calibration, through harmonic power, for Out and Opn objects
calibrate_harmonicpower_dfourier | Quantitative calibration, through harmonic power, for Out and Opn objects
calibrate_harmonicpower_efourier | Quantitative calibration, through harmonic power, for Out and Opn objects
calibrate_harmonicpower_rfourier | Quantitative calibration, through harmonic power, for Out and Opn objects
calibrate_harmonicpower_sfourier | Quantitative calibration, through harmonic power, for Out and Opn objects
calibrate_harmonicpower_tfourier | Quantitative calibration, through harmonic power, for Out and Opn objects
calibrate_r2 | Quantitative r2 calibration for Opn objects
calibrate_r2_npoly | Quantitative r2 calibration for Opn objects
calibrate_r2_opoly | Quantitative r2 calibration for Opn objects
calibrate_reconstructions | Calibrate using reconstructed shapes
calibrate_reconstructions_dfourier | Calibrate using reconstructed shapes
calibrate_reconstructions_efourier | Calibrate using reconstructed shapes
calibrate_reconstructions_npoly | Calibrate using reconstructed shapes
calibrate_reconstructions_opoly | Calibrate using reconstructed shapes
calibrate_reconstructions_rfourier | Calibrate using reconstructed shapes
calibrate_reconstructions_sfourier | Calibrate using reconstructed shapes
calibrate_reconstructions_tfourier | Calibrate using reconstructed shapes
chaff | Data: Landmark and semilandmark coordinates on cereal glumes
charring | Data: Outline coordinates from an experimental charring on cereal grains
chc2pix | Convert (x; y) coordinates to chaincoded coordinates
chop | Split to several objects based on a factor
classification_metrics | Calculate classification metrics on a confusion matrix
CLUST | Hierarchical clustering
CLUST.Coe | Hierarchical clustering
CLUST.default | 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 vector.
coeff_split | Converts a numerical description of harmonic coefficients to a named list.
color_palettes | Some color palettes
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 | Combine several objects
complex | Convert complex to/from cartesian coordinates
Coo | Coo "super" class
coo2cpx | Convert complex to/from cartesian coordinates
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_edges.Coo | Calculates the angle of every edge of a shape
coo_angle_edges.default | Calculates the angle of every edge of a shape
coo_angle_tangent | Calculates the tangent angle along the perimeter of a shape
coo_angle_tangent.Coo | Calculates the tangent angle along the perimeter of a shape
coo_angle_tangent.default | 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_centre | Centers coordinates
coo_centsize | Calculates centroid size
coo_check | Checks shapes
coo_chull | Calculates the (recursive) convex hull of a shape
coo_chull.Coo | Calculates the (recursive) convex hull of a shape
coo_chull.default | Calculates the (recursive) convex hull of a shape
coo_chull_onion | Calculates the (recursive) convex hull of a shape
coo_chull_onion.Coo | Calculates the (recursive) convex hull of a shape
coo_chull_onion.default | Calculates the (recursive) convex hull of a shape
coo_circularity | Calculates the Haralick's circularity of a shape
coo_circularity.Coo | Calculates the Haralick's circularity of a shape
coo_circularity.default | Calculates the Haralick's circularity of a shape
coo_circularityharalick | Calculates the Haralick's circularity of a shape
coo_circularityharalick.Coo | Calculates the Haralick's circularity of a shape
coo_circularityharalick.default | Calculates the Haralick's circularity of a shape
coo_circularitynorm | Calculates the Haralick's circularity of a shape
coo_circularitynorm.Coo | Calculates the Haralick's circularity of a shape
coo_circularitynorm.default | Calculates the Haralick's circularity of a shape
coo_close | Closes/uncloses shapes
coo_convexity | Calculates the convexity of a shape
coo_diffrange | Calculate coordinates range
coo_diffrange.Coo | Calculate coordinates range
coo_diffrange.default | Calculate coordinates range
coo_diffrange.list | Calculate coordinates range
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_eccentricityboundingbox | Calculates the eccentricity of a shape
coo_eccentricityboundingbox.Coo | Calculates the eccentricity of a shape
coo_eccentricityboundingbox.default | Calculates the eccentricity of a shape
coo_eccentricityeigen | Calculates the eccentricity of a shape
coo_eccentricityeigen.Coo | Calculates the eccentricity of a shape
coo_eccentricityeigen.default | Calculates the eccentricity 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_intersect_angle | Nearest intersection between a shape and a segment specified with an angle
coo_intersect_direction | Nearest intersection between a shape and a segment specified with an angle
coo_intersect_direction.Coo | Nearest intersection between a shape and a segment specified with an angle
coo_intersect_direction.default | Nearest intersection between a shape and a segment specified with an angle
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_anticlockwise | Tests if shapes are (likely) developping clockwise or anticlockwise
coo_likely_clockwise | Tests if shapes are (likely) developping clockwise or anticlockwise
coo_likely_clockwise.Coo | Tests if shapes are (likely) developping clockwise or anticlockwise
coo_likely_clockwise.default | Tests if shapes are (likely) developping clockwise or anticlockwise
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_perim.Coo | Calculates perimeter and variations
coo_perim.default | Calculates perimeter and variations
coo_perimcum | Calculates perimeter and variations
coo_perimcum.Coo | Calculates perimeter and variations
coo_perimcum.default | Calculates perimeter and variations
coo_perimpts | Calculates perimeter and variations
coo_perimpts.Coo | Calculates perimeter and variations
coo_perimpts.default | Calculates perimeter and variations
coo_plot | Plots a single shape
coo_range | Calculate coordinates range
coo_range.Coo | Calculate coordinates range
coo_range.default | Calculate coordinates range
coo_range_enlarge | Calculate coordinates range
coo_range_enlarge.Coo | Calculate coordinates range
coo_range_enlarge.default | Calculate coordinates range
coo_range_enlarge.list | 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_samplerr | Samples coordinates (regular radius)
coo_sample_prop | Sample a proportion of coordinates (among points)
coo_scalars | Calculates all scalar descriptors of shape
coo_scale | Scales coordinates
coo_scale.Coo | Scales coordinates
coo_scale.default | Scales coordinates
coo_scalex | Scales coordinates
coo_scalex.Coo | Scales coordinates
coo_scalex.default | Scales coordinates
coo_scaley | Scales coordinates
coo_scaley.Coo | Scales coordinates
coo_scaley.default | Scales coordinates
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_tac | Calculates the total absolute curvature of a shape
coo_tangle | Calculates the tangent angle along the perimeter of a shape
coo_template | 'Templates' shapes
coo_template.Coo | 'Templates' shapes
coo_template.default | 'Templates' shapes
coo_template.list | 'Templates' shapes
coo_template_relatively | 'Templates' shapes
coo_template_relatively.Coo | 'Templates' shapes
coo_template_relatively.list | '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_unclose | Closes/uncloses shapes
coo_untilt | Removes rotation so that the centroid and a given point are parallel to the x-axis
coo_untiltx | Removes rotation so that the centroid and a given point are parallel to the x-axis
coo_up | Retains coordinates with positive y-coordinates
coo_width | Calculates the width of a shape
cpx2coo | Convert complex to/from cartesian coordinates

## -- D --

d | A wrapper to calculates euclidean distances between two points
d2m | Convert between different classes
def_ldk | Defines new landmarks on Out and Opn objects
def_ldk_angle | Add new landmarks based on angular positions
def_ldk_direction | Add new landmarks based on angular positions
def_ldk_direction.default | Add new landmarks based on angular positions
def_ldk_direction.Opn | Add new landmarks based on angular positions
def_ldk_direction.Out | 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.Coo | Discrete cosinus transform
dfourier.default | Discrete cosinus transform
dfourier.list | Discrete cosinus transform
dfourier.Opn | 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
draw_axes | grindr drawers for shape plots
draw_centroid | grindr drawers for shape plots
draw_curve | grindr drawers for shape plots
draw_curves | grindr drawers for shape plots
draw_firstpoint | grindr drawers for shape plots
draw_labels | grindr drawers for shape plots
draw_landmarks | grindr drawers for shape plots
draw_lines | grindr drawers for shape plots
draw_links | grindr drawers for shape plots
draw_outline | grindr drawers for shape plots
draw_outlines | grindr drawers for shape plots
draw_points | grindr drawers for shape plots
draw_polygon | grindr drawers for shape plots
draw_ticks | grindr drawers for shape plots
draw_title | grindr drawers for shape plots

## -- E --

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 (and its normalization)
efourier.default | Elliptical Fourier transform (and its normalization)
efourier.list | Elliptical Fourier transform (and its normalization)
efourier.Out | Elliptical Fourier transform (and its normalization)
efourier_i | Inverse elliptical Fourier transform
efourier_norm | Elliptical Fourier transform (and its normalization)
efourier_shape | Calculates and draw 'efourier' shapes.
export | Exports Coe objects and shapes

## -- F --

fac_dispatcher | Brew and serve fac from Momocs object
fgProcrustes | Full Generalized Procrustes alignment between shapes
fgsProcrustes | Full Generalized Procrustes alignment between shapes with sliding landmarks
filter | Subset based on conditions
flip_PCaxes | Flips PCA axes
flower | Data: Measurement of iris flowers
fProcrustes | Full Procrustes alignment between two shapes

## -- G --

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

## -- H --

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

## -- I --

img_plot | Plots a .jpg image
img_plot0 | 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_curve | Import files creates by StereoMorph into Momocs
import_StereoMorph_curve1 | Import files creates by StereoMorph into Momocs
import_StereoMorph_ldk | Import files creates by StereoMorph into Momocs
import_StereoMorph_ldk1 | 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_Coe | Class and component testers
is_Coo | Class and component testers
is_equallyspacedradii | Tests if coordinates likely have equally spaced radii
is_fac | Class and component testers
is_LDA | Class and component testers
is_Ldk | Class and component testers
is_ldk | Class and component testers
is_LdkCoe | Class and component testers
is_links | Class and component testers
is_open | Test if shapes are closed
is_Opn | Class and component testers
is_OpnCoe | Class and component testers
is_Out | Class and component testers
is_OutCoe | Class and component testers
is_PCA | Class and component testers
is_shp | Class and component testers
is_slidings | Class and component testers
is_TraCoe | Class and component testers

## -- K --

KMEANS | KMEANS on PCA objects
KMEANS.PCA | KMEANS on PCA objects
KMEDOIDS | KMEDOIDS
KMEDOIDS.Coe | KMEDOIDS
KMEDOIDS.default | KMEDOIDS
KMEDOIDS.PCA | KMEDOIDS

## -- L --

l2a | Convert between different classes
l2m | Convert between different classes
layers | grindr layers for multivariate plots
layers_morphospace | Morphospace layers
layer_axes | grindr layers for multivariate plots
layer_axesnames | grindr layers for multivariate plots
layer_axesvar | grindr layers for multivariate plots
layer_box | grindr layers for multivariate plots
layer_chull | grindr layers for multivariate plots
layer_chullfilled | grindr layers for multivariate plots
layer_delaunay | grindr layers for multivariate plots
layer_density | grindr layers for multivariate plots
layer_density_2 | grindr layers for multivariate plots
layer_eigen | grindr layers for multivariate plots
layer_ellipses | grindr layers for multivariate plots
layer_ellipsesaxes | grindr layers for multivariate plots
layer_ellipsesfilled | grindr layers for multivariate plots
layer_frame | grindr layers for multivariate plots
layer_fullframe | grindr layers for multivariate plots
layer_grid | grindr layers for multivariate plots
layer_histogram_2 | grindr layers for multivariate plots
layer_labelgroups | grindr layers for multivariate plots
layer_labelpoints | grindr layers for multivariate plots
layer_legend | grindr layers for multivariate plots
layer_morphospace_LDA | Morphospace layers
layer_morphospace_PCA | Morphospace layers
layer_points | grindr layers for multivariate plots
layer_rug | grindr layers for multivariate plots
layer_stars | grindr layers for multivariate plots
layer_ticks | grindr layers for multivariate plots
layer_title | grindr layers for multivariate plots
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
LdkCoe | 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 | 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

## -- M --

m2a | Convert between different classes
m2d | Convert between different classes
m2l | Convert between different classes
m2ll | Convert between different classes
MANOVA | Multivariate analysis of (co)variance on Coe objects
MANOVA.OpnCoe | Multivariate analysis of (co)variance on Coe objects
MANOVA.OutCoe | Multivariate analysis of (co)variance on Coe objects
MANOVA.PCA | Multivariate analysis of (co)variance on Coe objects
MANOVA_PW | Pairwise Multivariate analyses of variance
MANOVA_PW.PCA | Pairwise Multivariate analyses of variance
MDS | (Metric) multidimensional scaling
measure | Measures shape descriptors
molars | Data: Outline coordinates of 360 molars
Momocs | Momocs
morphospace_positions | Calculates nice positions on a plane for drawing shapes
mosaic | Plots mosaics of shapes.
mosaic.Ldk | Plots mosaics of shapes.
mosaic.Opn | Plots mosaics of shapes.
mosaic.Out | Plots mosaics of shapes.
mosaic_engine | Plots mosaics of shapes.
mosquito | Data: Outline coordinates of mosquito wings.
mouse | Data: Outline coordinates of mouse molars
MSHAPES | Mean shape calculation for Coo, Coe, etc.
mutate | Add new variables

## -- N --

NMDS | Non metric multidimensional scaling
npoly | Calculate natural polynomial fits on open outlines
npoly.default | Calculate natural polynomial fits on open outlines
npoly.list | Calculate natural polynomial fits on open outlines
npoly.Opn | Calculate natural polynomial fits on open outlines
npoly_i | Calculates shape from a polynomial model
nsfishes | Data: Outline coordinates of North Sea fishes

## -- O --

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.list | 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

## -- P --

pal | Color palettes
palette | Color palettes
Palettes | Some color palettes
palettes | Color palettes
pal_alpha | Color palettes
pal_div | Color palettes
pal_div_BrBG | Color palettes
pal_div_PiYG | Color palettes
pal_div_PRGn | Color palettes
pal_div_PuOr | Color palettes
pal_div_RdBu | Color palettes
pal_div_RdYlBu | Color palettes
pal_manual | Color palettes
pal_qual | Color palettes
pal_qual_Dark2 | Color palettes
pal_qual_Paired | Color palettes
pal_qual_Set2 | Color palettes
pal_qual_solarized | Color palettes
pal_seq | Color palettes
pal_seq_Blues | Color palettes
pal_seq_BuGn | Color palettes
pal_seq_BuPu | Color palettes
pal_seq_GnBu | Color palettes
pal_seq_Greens | Color palettes
pal_seq_grey | Color palettes
pal_seq_Greys | Color palettes
pal_seq_inferno | Color palettes
pal_seq_magma | Color palettes
pal_seq_Oranges | Color palettes
pal_seq_OrRd | Color palettes
pal_seq_plasma | Color palettes
pal_seq_PuBu | Color palettes
pal_seq_PuBuGn | Color palettes
pal_seq_PuRd | Color palettes
pal_seq_Purples | Color palettes
pal_seq_RdPu | Color palettes
pal_seq_Reds | Color palettes
pal_seq_viridis | Color palettes
pal_seq_YlGn | Color palettes
pal_seq_YlGnBu | Color palettes
pal_seq_YlOrBr | Color palettes
pal_seq_YlOrRd | 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
paper | grindr papers for shape plots
papers | grindr papers for shape plots
paper_chess | grindr papers for shape plots
paper_dots | grindr papers for shape plots
paper_grid | grindr papers for shape plots
paper_white | grindr papers for shape plots
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
pile | Graphical pile of shapes
pile.array | Graphical pile of shapes
pile.default | Graphical pile of shapes
pile.Ldk | Graphical pile of shapes
pile.list | Graphical pile of shapes
pile.Opn | Graphical pile of shapes
pile.Out | Graphical pile of shapes
pix2chc | Convert (x; y) coordinates to chaincoded coordinates
plot.LDA | Plots Linear Discriminant Analysis
plot.PCA | Plots Principal Component Analysis
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.
plot_LDA | LDA plot using grindr layers
plot_MDS | NMDS plot unsing grindr layers
plot_MSHAPES | Pairwise comparison of a list of shapes
plot_NMDS | NMDS plot unsing grindr layers
plot_PCA | PCA plot using grindr layers
plot_silhouette | Silhouette plot
plot_table | Plots confusion matrix of sample sizes within $fac
pProcrustes | Partial Procrustes alignment between two shapes
Ptolemy | Ptolemaic ellipses and illustration of efourier

## -- R --

rearrange_ldk | Rearrange, (select and reorder) landmarks to retain
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 | 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.default | Radii variation Fourier transform (equally spaced radii)
rfourier.list | Radii variation Fourier transform (equally spaced radii)
rfourier.Out | 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_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_missing | Remove shapes with missing data in fac
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 | Remove shapes with incomplete slices
rw_fac | Renames levels on Momocs objects

## -- S --

sample_frac | Sample a fraction of shapes
sample_n | Sample n shapes
scree | How many axes to retain this much of variance or trace ?
scree.LDA | How many axes to retain this much of variance or trace ?
scree.PCA | How many axes to retain this much of variance or trace ?
scree_min | How many axes to retain this much of variance or trace ?
scree_plot | How many axes to retain this much of variance or trace ?
select | Select columns by name
sfourier | Radii variation Fourier transform (equally spaced curvilinear abscissa)
sfourier.default | Radii variation Fourier transform (equally spaced curvilinear abscissa)
sfourier.list | Radii variation Fourier transform (equally spaced curvilinear abscissa)
sfourier.Out | 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 | Subset based on positions
slidings_scheme | Extracts partitions of sliding coordinates
stack | Family picture of shapes
stack.Coo | Family picture of shapes
stack.Ldk | Family picture of shapes
subsetize | Subsetize various Momocs objects
symmetry | Calcuates symmetry indices on OutCoe objects

## -- T --

tfourier | Tangent angle Fourier transform
tfourier.default | Tangent angle Fourier transform
tfourier.list | 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 | Import a tps file
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
trilo | Data: Outline coordinates of cephalic outlines of trilobite

## -- V --

verify | Validates Coo objects

## -- W --

which_out | Identify outliers
wings | Data: Landmarks coordinates of mosquito wings