Function reference • Momocs

All functions

CLUST(): Hierarchical clustering

Coe(): Coe "super" class

Coo(): Coo "super" class

KMEANS(): KMEANS on PCA objects

KMEDOIDS(): KMEDOIDS

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

MDS(): (Metric) multidimensional scaling

MSHAPES(): Mean shape calculation for Coo, Coe, etc.

Momocs: Momocs

NMDS(): Non metric multidimensional scaling

Opn(): Builds an Opn object

OpnCoe(): Builds an OpnCoe object

Out(): Builds an Out object

OutCoe(): Builds an OutCoe object

PCA() as_PCA(): Principal component analysis on Coe objects

PCcontrib(): Shape variation along PC axes

Ptolemy(): Ptolemaic ellipses and illustration of efourier

TraCoe(): Traditional morphometrics class

add_ldk(): Adds new landmarks on Out and Opn objects

arrange(): Arrange rows by variables

as_df(): Turn Momocs objects into tydy data_frames

at_least(): Retain groups with at least n shapes

pix2chc() chc2pix(): Convert (x; y) coordinates to chaincoded coordinates

bezier(): Calculates Bezier coefficients from a shape

bezier_i(): Calculates a shape from Bezier coefficients

boxplot(<OutCoe>): Boxplot of morphometric coefficients

boxplot(<PCA>): Boxplot on PCA objects

breed(): Jitters Coe (and others) objects

l2m() m2l() d2m() m2d() l2a() a2l() a2m() m2a() m2ll(): Convert between different classes

calibrate_deviations() calibrate_deviations_efourier() calibrate_deviations_tfourier() calibrate_deviations_rfourier() calibrate_deviations_sfourier() calibrate_deviations_npoly() calibrate_deviations_opoly() calibrate_deviations_dfourier(): Quantitative calibration, through deviations, for Out and Opn objects

calibrate_harmonicpower() calibrate_harmonicpower_efourier() calibrate_harmonicpower_rfourier() calibrate_harmonicpower_tfourier() calibrate_harmonicpower_sfourier() calibrate_harmonicpower_dfourier(): Quantitative calibration, through harmonic power, for Out and Opn objects

calibrate_r2() calibrate_r2_opoly() calibrate_r2_npoly(): Quantitative r2 calibration for Opn objects

calibrate_reconstructions_efourier() calibrate_reconstructions_rfourier() calibrate_reconstructions_tfourier() calibrate_reconstructions_sfourier() calibrate_reconstructions_npoly() calibrate_reconstructions_opoly() calibrate_reconstructions_dfourier(): Calibrate using reconstructed shapes

chop(): Split to several objects based on a factor

classification_metrics(): Calculate classification metrics on a confusion matrix

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() col_summer2() col_spring() col_autumn() col_black() col_solarized() col_gallus() col_qual() col_heat() col_hot() col_cold() col_sari() col_india() col_bw() col_grey(): Some color palettes

col_transp() col_alpha(): Transparency helpers and palettes

combine(): Combine several objects

cpx2coo() 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_tangent() coo_tangle(): 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() coo_centre(): Centers coordinates

coo_centpos(): Calculate centroid coordinates

coo_centsize(): Calculates centroid size

coo_check(): Checks shapes

coo_chull() coo_chull_onion(): Calculates the (recursive) convex hull of a shape

coo_circularity() coo_circularityharalick() coo_circularitynorm(): Calculates the Haralick's circularity of a shape

coo_close() coo_unclose(): 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_draw_rads(): Draw radii to the current plot

coo_dxy(): Calculate abscissa and ordinate on a shape

coo_eccentricityeigen() coo_eccentricityboundingbox(): Calculates the eccentricity of a shape

coo_elongation(): Calculates the elongation of a shape

coo_extract(): Extract coordinates from a shape

coo_flipx() coo_flipy(): Flips shapes

coo_force2close(): Forces shapes to close

coo_interpolate(): Interpolates coordinates

coo_intersect_angle() coo_intersect_direction(): 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() is_open(): 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_clockwise() coo_likely_anticlockwise(): 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_perimpts() coo_perimcum() coo_perim(): Calculates perimeter and variations

coo_plot() ldk_plot(): Plots a single shape

coo_range() coo_range_enlarge() coo_diffrange(): 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_sample_prop(): Sample a proportion of coordinates (among points)

coo_samplerr(): Samples coordinates (regular radius)

coo_scalars(): Calculates all scalar descriptors of shape

coo_scale() coo_scalex() coo_scaley(): Scales coordinates

coo_shearx() 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_template() coo_template_relatively(): '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_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

d(): A wrapper to calculates euclidean distances between two points

apodemus: Data: Outline coordinates of Apodemus (wood mouse) mandibles

bot: Data: Outline coordinates of beer and whisky bottles.

chaff: Data: Landmark and semilandmark coordinates on cereal glumes

charring: Data: Outline coordinates from an experimental charring on cereal grains

flower: Data: Measurement of iris flowers

hearts: Data: Outline coordinates of hand-drawn hearts

molars: Data: Outline coordinates of 360 molars

mosquito: Data: Outline coordinates of mosquito wings.

mouse: Data: Outline coordinates of mouse molars

nsfishes: Data: Outline coordinates of North Sea fishes

oak: Data: Configuration of landmarks of oak leaves

olea: Data: Outline coordinates of olive seeds open outlines.

shapes: Data: Outline coordinates of various shapes

trilo: Data: Outline coordinates of cephalic outlines of trilobite

wings: Data: Landmarks coordinates of mosquito wings

def_ldk(): Defines new landmarks on Out and Opn objects

def_ldk_angle() def_ldk_direction(): 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_i(): Investe discrete cosinus transform

dfourier_shape(): Calculates and draws 'dfourier' shapes

dissolve(): Dissolve Coe objects

draw_polygon() draw_outline() draw_outlines() draw_points() draw_landmarks() draw_lines() draw_centroid() draw_curve() draw_curves() draw_firstpoint() draw_axes() draw_ticks() draw_labels() draw_links() draw_title(): grindr drawers for shape plots

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() efourier_norm(): Elliptical Fourier transform (and its normalization)

efourier_i(): Inverse elliptical Fourier transform

efourier_shape(): Calculates and draw 'efourier' shapes.

export(): Exports Coe objects and shapes

fProcrustes(): Full Procrustes alignment between two shapes

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

get_chull_area() 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

hcontrib(): Harmonic contribution to shape

harm_pow(): Calculates harmonic power given a list from e/t/rfourier

img_plot() img_plot0(): Plots a .jpg image

import_Conte(): Extract outlines coordinates from an image silhouette

import_StereoMorph_curve1() import_StereoMorph_curve() import_StereoMorph_ldk1() import_StereoMorph_ldk(): Import files creates by StereoMorph into Momocs

import_jpg(): Extract outline coordinates from multiple .jpg files

import_jpg1(): Extract outline coordinates from a single .jpg file

import_tps() tps2coo(): Import a tps file

import_txt(): Import coordinates from a .txt file

inspect(): Graphical inspection of shapes

is_Coo() is_PCA() is_LDA() is_Out() is_Opn() is_Ldk() is_Coe() is_OutCoe() is_OpnCoe() is_LdkCoe() is_TraCoe() is_shp() is_fac() is_ldk() is_slidings() is_links(): Class and component testers

is_equallyspacedradii(): Tests if coordinates likely have equally spaced radii

layer_frame() layer_axes() layer_ticks() layer_grid() layer_box() layer_fullframe() layer_points() layer_ellipses() layer_ellipsesfilled() layer_ellipsesaxes() layer_chull() layer_chullfilled() layer_stars() layer_delaunay() layer_density() layer_labelpoints() layer_labelgroups() layer_rug() layer_histogram_2() layer_density_2() layer_title() layer_axesnames() layer_eigen() layer_axesvar() layer_legend(): grindr layers for multivariate plots

layer_morphospace_PCA() layer_morphospace_LDA(): Morphospace layers

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(): 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

measure(): Measures shape descriptors

morphospace_positions(): Calculates nice positions on a plane for drawing shapes

mosaic_engine() mosaic(): Plots mosaics of shapes.

mutate(): Add new variables

npoly(): Calculate natural polynomial fits on open outlines

opoly(): Calculate orthogonal polynomial fits on open outlines

pProcrustes(): Partial Procrustes alignment between two shapes

pal_alpha() pal_manual() pal_qual_solarized() pal_seq_grey() pal_div_BrBG() pal_div_PiYG() pal_div_PRGn() pal_div_PuOr() pal_div_RdBu() pal_div_RdYlBu() pal_qual_Dark2() pal_qual_Paired() pal_qual_Set2() pal_seq_Blues() pal_seq_BuGn() pal_seq_BuPu() pal_seq_GnBu() pal_seq_Greens() pal_seq_Greys() pal_seq_Oranges() pal_seq_OrRd() pal_seq_PuBu() pal_seq_PuBuGn() pal_seq_PuRd() pal_seq_Purples() pal_seq_RdPu() pal_seq_Reds() pal_seq_YlGn() pal_seq_YlGnBu() pal_seq_YlOrBr() pal_seq_YlOrRd() pal_seq_magma() pal_seq_inferno() pal_seq_plasma() pal_seq_viridis() pal_qual() pal_seq() pal_div(): Color palettes

panel(): Family picture of shapes

paper() paper_white() paper_grid() paper_chess() paper_dots(): grindr papers for shape plots

perm(): Permutes and breed Coe (and others) objects

pile(): Graphical pile of shapes

plot(<LDA>): Plots Linear Discriminant Analysis

plot(<PCA>): Plots Principal Component Analysis

plot_CV(): Plots a cross-validation table as an heatmap

plot_CV2(): Plots a cross-correlation table

plot_LDA(): LDA plot using grindr layers

plot_MSHAPES(): Pairwise comparison of a list of shapes

plot_NMDS() plot_MDS(): NMDS plot unsing grindr layers

plot_PCA(): PCA plot using grindr layers

plot_devsegments(): Draws colored segments from a matrix of coordinates.

plot_silhouette(): Silhouette plot

plot_table(): Plots confusion matrix of sample sizes within $fac

opoly_i() npoly_i(): Calculates shape from a polynomial model

reLDA(): "Redo" a LDA on new data

rePCA(): "Redo" a PCA on a new Coe

rearrange_ldk(): Rearrange, (select and reorder) landmarks to retain

rename(): Rename columns by name

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() rm_sym(): 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_uncomplete(): Remove shapes with incomplete slices

rw_fac(): Renames levels on Momocs objects

sample_frac(): Sample a fraction of shapes

sample_n(): Sample n shapes

scree() scree_min() 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_i(): Inverse radii variation Fourier transform

sfourier_shape(): Calculates and draw 'sfourier' shapes.

slice(): Subset based on positions

slidings_scheme(): Extracts partitions of sliding coordinates

stack(<Coo>) stack(<Ldk>): Family picture of shapes

subsetize(): Subsetize various Momocs objects

symmetry(): Calcuates symmetry indices on OutCoe 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

tps2d() 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

verify(): Validates Coo objects

which_out(): Identify outliers