Morphometrics using R


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Documentation for package ‘Momocs’ version 1.2.2

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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
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.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
classification_metrics Calculate classification metrics on a confusion matrix
classify Classify using LDA
CLUST 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.
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
coo2cpx Converts cartesian to complex 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_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 convex hull of a shape
coo_chull_onion Peeling points by recursively removing their convex hulls
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_draw_rads Draw radii 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
cpx2coo Converts complex to cartesian coordinates

-- D --

d A wrapper to calculates euclidean distances between two points
d2m Converts a data.frame of coordinates to a matrix of coordinates.
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
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
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_anticlockwise Tests if shapes are developping clockwise or anticlockwise
is_clockwise Tests if shapes are developping clockwise or anticlockwise
is_closed Tests if shapes are closed
is_Coe Various class/component testers
is_Coo Various class/component testers
is_equallyspacedradii Tests if coordinates likely have equally spaced radii
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_open Tests if shapes are closed
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_TraCoe Various class/component testers

-- 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
list_classes_for_this_method List available methods for any object and other classes for a method
list_methods_for_this_class List available methods for any object and other classes for a method

-- M --

m2a Converts a matrix of coordinates to an array of coordinates
m2d Converts a matrix of coordinates to a two-columns 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_currentCRANversion Install and load the last version of Momocs
Momocs_currentGitHubversion Install and load the last version of Momocs
Momocs_help Browse Momocs online doc
Momocs_lastversion Install and load the last version of Momocs
Momocs_version Install and load the last version of Momocs
mosquito Data: Outline coordinates of mosquito wings.
mouse Data: Outline coordinates of mouse molars
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
nsfishes Data: Outline coordinates of North Sea fishes
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.
plot_mshapes Pairwise comparison of a list of shapes
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 --

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 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 (equally spaced radii)
rfourier.default 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_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_fac Renames levels on Momocs objects
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
sfourier Radii variation Fourier transform (equally spaced curvilinear abscissa)
sfourier.default 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 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
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 Identify outliers
wings Data: Landmarks coordinates of mosquito wings