# Morphometrics using R

## Documentation for package ‘Momocs’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

Momocs-package | Momocs

## -- A --

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.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

## -- B --

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

## -- C --

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 both ends coordinates from shape
coo_trimbottom | Trims bottom coordinates from shape
coo_trimtop | Trims top 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 --

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.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

## -- 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
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

## -- F --

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

## -- 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
hist.Coe | Histogram of morphometric coefficients
hist.OutCoe | Histogram of morphometric coefficients

## -- I --

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

## -- K --

KMEANS | KMEANS on PCA objects
KMEANS.PCA | KMEANS on PCA objects

## -- L --

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

## -- M --

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.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
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

## -- N --

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

## -- 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.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 --

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

## -- R --

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

## -- S --

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

## -- T --

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

## -- V --

validate | Validates Coo objects
vecs_param | Some vector utilities.

## -- W --

which_out | Remove outliers on Coe
wings | Data: Landmarks coordinates of mosquito wings