Package index • Momocs

Morphometrics methods

efourier() efourier_norm(): Elliptical Fourier transform (and its normalization)
rfourier(): Radii variation Fourier transform (equally spaced radii)
tfourier(): Tangent angle Fourier transform
sfourier(): Radii variation Fourier transform (equally spaced curvilinear abscissa)
dfourier(): Discrete cosinus transform
opoly(): Calculate orthogonal polynomial fits on open outlines
npoly(): Calculate natural polynomial fits on open outlines
fgProcrustes(): Full Generalized Procrustes alignment between shapes
fgsProcrustes(): Full Generalized Procrustes alignment between shapes with sliding landmarks
bezier(): Calculates Bezier coefficients from a shape

More morphometrics methods

Inverse functions and some others internally used by the main ones

efourier_i(): Inverse elliptical Fourier transform
rfourier_i(): Inverse radii variation Fourier transform
tfourier_i(): Inverse tangent angle Fourier transform
sfourier_i(): Inverse radii variation Fourier transform
dfourier_i(): Investe discrete cosinus transform
opoly_i() npoly_i(): Calculates shape from a polynomial model
bezier_i(): Calculates a shape from Bezier coefficients
fProcrustes(): Full Procrustes alignment between two shapes
pProcrustes(): Partial Procrustes alignment between two shapes

Calibration and other helpers for (open or not) outlines

When defined

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_reconstructions_efourier() calibrate_reconstructions_rfourier() calibrate_reconstructions_tfourier() calibrate_reconstructions_sfourier() calibrate_reconstructions_npoly() calibrate_reconstructions_opoly() calibrate_reconstructions_dfourier(): Calibrate using reconstructed shapes
calibrate_r2() calibrate_r2_opoly() calibrate_r2_npoly(): Quantitative r2 calibration for Opn objects
harm_pow(): Calculates harmonic power given a list from e/t/rfourier
hcontrib(): Harmonic contribution to shape
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.
rm_asym() rm_sym(): Removes asymmetric and symmetric variation on OutCoe objects
symmetry(): Calcuates symmetry indices on OutCoe objects
Ptolemy(): Ptolemaic ellipses and illustration of efourier
morphospace_positions(): Calculates nice positions on a plane for drawing shapes

Classes

Their description and rationale

Coo(): Coo "super" class
Out(): Builds an Out object
Opn(): Builds an Opn object
Ldk(): Builds an Ldk object
Coe(): Coe "super" class
OutCoe(): Builds an OutCoe object
OpnCoe(): Builds an OpnCoe object
TraCoe(): Traditional morphometrics class
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

Classes manipulation

Largely inspired from dplyr’s verbs

arrange(): Arrange rows by variables
at_least(): Retain groups with at least n shapes
chop(): Split to several objects based on a factor
combine(): Combine several objects
dissolve(): Dissolve Coe objects
filter(): Subset based on conditions
mutate(): Add new variables
rescale(): Rescale coordinates from pixels to real length units
rename(): Rename columns by name
select(): Select columns by name
rm_harm(): Removes harmonics from Coe objects
rm_uncomplete(): Remove shapes with incomplete slices
rm_missing(): Remove shapes with missing data in fac
rw_fac(): Renames levels on Momocs objects
sample_frac(): Sample a fraction of shapes
sample_n(): Sample n shapes
slice(): Subset based on positions
subsetize(): Subsetize various Momocs objects
verify(): Validates Coo objects

Import/Export

Will be all moved to Momit soon

export(): Exports Coe objects and shapes
as_df(): Turn Momocs objects into tydy data_frames
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_curve1() import_StereoMorph_curve() import_StereoMorph_ldk1() import_StereoMorph_ldk(): Import files creates by StereoMorph into Momocs
import_tps() tps2coo(): Import a tps file
import_txt(): Import coordinates from a .txt file
tie_jpg_txt(): Binds .jpg outlines from .txt landmarks taken on them
img_plot() img_plot0(): Plots a .jpg image
lf_structure(): bind_db.Coe <- bind_db.Coo Extracts structure from filenames
pix2chc() chc2pix(): Convert (x; y) coordinates to chaincoded coordinates

Multivariate methods

Will be in Momecs at some point, and with KMEDOIDS, SVM, NNET and QDA

PCA() as_PCA(): Principal component analysis on Coe objects
LDA(): Linear Discriminant Analysis on Coe objects
MSHAPES(): Mean shape calculation for Coo, Coe, etc.
MANOVA(): Multivariate analysis of (co)variance on Coe objects
MANOVA_PW(): Pairwise Multivariate analyses of variance
KMEANS(): KMEANS on PCA objects
KMEDOIDS(): KMEDOIDS
MDS(): (Metric) multidimensional scaling
NMDS(): Non metric multidimensional scaling
CLUST(): Hierarchical clustering

More on multivariate

Will be in Momecs at some point

PCcontrib(): Shape variation along PC axes
flip_PCaxes(): Flips PCA axes
scree() scree_min() scree_plot(): How many axes to retain this much of variance or trace ?
rePCA(): "Redo" a PCA on a new Coe
reLDA(): "Redo" a LDA on new data
classification_metrics(): Calculate classification metrics on a confusion matrix
which_out(): Identify outliers
plot(<LDA>): Plots Linear Discriminant Analysis
plot(<PCA>): Plots Principal Component Analysis
boxplot(<OutCoe>): Boxplot of morphometric coefficients
boxplot(<PCA>): Boxplot on PCA objects

Graphics

Because who does not love graphics?

panel(): Family picture of shapes
mosaic_engine() mosaic(): Plots mosaics of shapes.
pile(): Graphical pile of shapes
stack(<Coo>) stack(<Ldk>): Family picture of shapes
inspect(): Graphical inspection of shapes
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
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

grindr Graphics

(base) graphics is not dead!

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

Bridges

Convert between different classes

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

Landmark helpers

add_ldk(): Adds new landmarks on Out and Opn objects
coo_plot() ldk_plot(): Plots a single shape
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
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
links_all(): Creates links (all pairwise combinations) between landmarks
links_delaunay(): Creates links (Delaunay triangulation) between landmarks
d(): A wrapper to calculates euclidean distances between two points
measure(): Measures shape descriptors
coo_truss(): Truss measurement
slidings_scheme(): Extracts partitions of sliding coordinates
rearrange_ldk(): Rearrange, (select and reorder) landmarks to retain

Getters/Setters for components of interest

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

Data

To play around with various data types

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

Farming shapes

Most of them will move to Momfarm soon

dfourier_shape(): Calculates and draws 'dfourier' shapes
efourier_shape(): Calculates and draw 'efourier' shapes.
rfourier_shape(): Calculates and draw 'rfourier' shapes.
sfourier_shape(): Calculates and draw 'sfourier' shapes.
tfourier_shape(): Calculates and draws 'tfourier' shapes.
breed(): Jitters Coe (and others) objects
perm(): Permutes and breed Coe (and others) objects

Color palettes

Qualitative, diverging and sequential, all those colorblind friendly from RColorBrewer, viridis and more.

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
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

Misc

Momocs-package Momocs: Momocs
cpx2coo() coo2cpx(): Convert complex to/from cartesian coordinates
ed(): Calculates euclidean distance 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.
edi(): Calculates euclidean intermediate between two points.
is_equallyspacedradii(): Tests if coordinates likely have equally spaced radii
fac_dispatcher(): Brew and serve fac from Momocs object

coo_ toolbox

circa 100 helpers for 2D shapes and Coo objects

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