Morphometrics using R

add_ldk | Adds new landmarks on Out and Opn objects |

andnow | And now, what to do? |

arrange | Arrange rows by variables |

as_df | Converts Momocs objects to data.frames |

at_least | Retain groups with at least n shapes |

babel | 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 |

bridges | Convert between different classes |

calibrate_deviations | Quantitative calibration, through deviations, for Out and Opn... |

calibrate_harmonicpower | Quantitative calibration, through harmonic power, for Out and... |

calibrate_r2 | Quantitative r2 calibration for Opn objects |

calibrate_reconstructions | Calibrate using reconstructed shapes |

chop | Split to several objects based on a factor |

classification_metrics | Calculate classification metrics on a confusion matrix |

CLUST | 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... |

coeff_split | Converts a numerical description of harmonic coefficients to... |

color_palettes | Some color palettes |

color_transparency | Transparency helpers and palettes |

combine | Combine several objects |

complex | Convert complex to/from cartesian coordinates |

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_angle_edge1 | Calculate the angle formed by three (x; y) coordinates |

coo_angle_edges | Calculates the angle of every edge of a shape |

coo_angle_tangent | 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_centsize | Calculates centroid size |

coo_check | Checks shapes |

coo_chull | Calculates the (recursive) convex hull of a shape |

coo_circularity | Calculates the Haralick's 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_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_elongation | Calculates the elongation of a shape |

coo_extract | Extract coordinates from a shape |

coo_flip | Flips shapes |

coo_force2close | Forces shapes to close |

coo_interpolate | Interpolates coordinates |

coo_intersect_angle | Nearest intersection between a shape and a segment specified... |

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_clockwise | Tests if shapes are (likely) developping clockwise or... |

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_plot | Plots a single shape |

coo_range | 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_scale | Scales coordinates |

coo_shear | 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 | '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... |

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... |

data_apodemus | Data: Outline coordinates of Apodemus (wood mouse) mandibles |

data_bot | Data: Outline coordinates of beer and whisky bottles. |

data_chaff | Data: Landmark and semilandmark coordinates on cereal glumes |

data_charring | Data: Outline coordinates from an experimental charring on... |

data_flower | Data: Measurement of iris flowers |

data_hearts | Data: Outline coordinates of hand-drawn hearts |

data_molars | Data: Outline coordinates of 360 molars |

data_mosquito | Data: Outline coordinates of mosquito wings. |

data_mouse | Data: Outline coordinates of mouse molars |

data_nsfishes | Data: Outline coordinates of North Sea fishes |

data_oak | Data: Configuration of landmarks of oak leaves |

data_olea | Data: Outline coordinates of olive seeds open outlines. |

data_shapes | Data: Outline coordinates of various shapes |

data_trilo | Data: Outline coordinates of cephalic outlines of trilobite |

data_wings | Data: Landmarks coordinates of mosquito wings |

def_ldk | Defines new landmarks on Out and Opn objects |

def_ldk_angle | 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 |

drawers | 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... |

edm_nearest | Calculates the shortest euclidean distance found for every... |

efourier | 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 |

fac_dispatcher | Brew and serve fac from Momocs object |

fgProcrustes | Full Generalized Procrustes alignment between shapes |

fgsProcrustes | Full Generalized Procrustes alignment between shapes with... |

filter | Subset based on conditions |

flip_PCaxes | Flips PCA axes |

fProcrustes | Full Procrustes alignment between two shapes |

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.contrib | Harmonic contribution to shape |

harm_pow | Calculates harmonic power given a list from e/t/rfourier |

hist.OutCoe | Histogram of morphometric coefficients |

img_plot | 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 | 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_equallyspacedradii | Tests if coordinates likely have equally spaced radii |

KMEANS | KMEANS on PCA objects |

KMEDOIDS | KMEDOIDS |

layers | grindr layers for multivariate plots |

layers_morphospace | Morphospace layers |

LDA | 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 |

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 |

MANOVA | Multivariate analysis of (co)variance on Coe objects |

MANOVA_PW | Pairwise Multivariate analyses of variance |

MDS | (Metric) multidimensional scaling |

measure | Measures shape descriptors |

Momocs | Momocs |

Momocs_help | Browse Momocs online doc |

Momocs_version | Install last version of Momocs |

morphospace_positions | Calculates nice positions on a plane for drawing shapes |

mosaic | Plots mosaics of shapes. |

MSHAPES | Mean shape calculation for Coo, Coe, etc. |

mutate | Add new variables |

NMDS | Non metric multidimensional scaling |

npoly | Calculate natural polynomial fits on open outlines |

Opn | Builds an Opn object |

OpnCoe | Builds an OpnCoe object |

opoly | Calculate orthogonal polynomial fits on open outlines |

Out | Builds an Out object |

OutCoe | Builds an OutCoe object |

palettes | Color palettes |

panel.Coo | Family picture of shapes |

papers | grindr papers for shape plots |

PCA | Principal component analysis on Coe objects |

PCcontrib | Shape variation along PC axes |

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

pile | Graphical pile of shapes |

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_LDA | LDA plot using grindr layers |

plot.LDA | Plots Linear Discriminant Analysis |

plot_MSHAPES | Pairwise comparison of a list of shapes |

plot_NMDS | NMDS plot unsing grindr layers |

plot_PCA | PCA plot using grindr layers |

plot.PCA | Plots Principal Component Analysis |

plot_silhouette | Silhouette plot |

plot_table | Plots confusion matrix of sample sizes within $fac |

poly_i | Calculates shape from a polynomial model |

pProcrustes | Partial Procrustes alignment between two shapes |

Ptolemy | Ptolemaic ellipses and illustration of efourier |

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

reexports | Objects exported from other packages |

reLDA | "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_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_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 | Methods for PCA eigen values |

select | Select columns by name |

sfourier | Radii variation Fourier transform (equally spaced curvilinear... |

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 | Family picture of shapes |

subset | 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 | 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 |

verify | Validates Coo objects |

which_out | Identify outliers |

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