Man pages for vbonhomme/Momocs
Morphometrics using R

a2lConverts an array of coordinates to a list of matrices
a2mConverts an array of coordinates to a matrix
add_ldkAdds new landmarks on Out and Opn objects
arrangeArranges (ala dplyr) on Momocs objects
as_dfConverts Momocs objects to data.frames
as.OutConvert an OutCoe object into an Out object
at_leastRetains group with at least a certain number of individuals
bezierCalculates Bezier coefficients from a shape
bezier_iCalculates a shape from Bezier coefficients
bind_dbBinds with a database
boxplot.OutCoeBoxplot of morphometric coefficients
boxplot.PCABoxplot on PCA objects
breedJitters Coe (and others) objects
calibrate_deviationsQuantitative calibration, through deviations, for Out and Opn...
calibrate_harmonicpowerQuantitative calibration, through harmonic power, for Out and...
calibrate_r2Quantitative r2 calibration for Opn objects
calibrate_reconstructionsCalibrate using reconstructed shapes
chc2OutConverts chain-coded coordinates to Out object
chc2pixConverts chain-coded coordinates to (x; y) coordinates
chopChops (rough slicing) Momocs objects
classification_metricsCalculate classification metrics on a confusion matrix
classifyClassify using LDA
CLUSTHierarchical clustering
CoeCoe "super" class
coeff_rearrangeRearrange a matrix of (typically Fourier) coefficients
coeff_selHelps to select a given number of harmonics from a numerical...
coeff_splitConverts a numerical description of harmonic coefficients to...
color_palettesSome color palettes
colors_transpTransparency helpers and palettes
combineCombines Momocs objects
conf_ellConfidence ellipses
CooCoo "super" class
coo2cpxConverts cartesian to complex coordinates
coo_alignAligns coordinates
coo_aligncalliperAligns shapes along their 'calliper length'
coo_alignminradiusAligns shapes using their shortest radius
coo_alignxaxAligns shapes along the x-axis
coo_areaCalculates the area of a shape
coo_arrowsPlots (lollipop) differences between two configurations
coo_baselineRegister new baselines
coo_booksteinRegister Bookstein's coordinates
coo_boundingboxCalculates coordinates of the bounding box
coo_calliperCalculates the calliper length
coo_centdistReturns the distance between everypoints and the centroid
coo_centerCenters coordinates
coo_centposCalculate centroid coordinates
coo_centsizeCalculates centroid size
coo_checkChecks shapes
coo_chullCalculates the convex hull of a shape
coo_chull_onionPeeling points by recursively removing their convex hulls
coo_circularityCalculates the circularity of a shape
coo_circularityharalickCalculates the Haralick's circularity of a shape
coo_circularitynormCalculates the 'normalized' circularity of a shape
coo_closeCloses/uncloses shapes
coo_convexityCalculates the convexity of a shape
coo_downcoo_down —- Retains coordinates with negative y-coordinates
coo_drawAdds a shape to the current plot
coo_draw_radsDraw radii to the current plot
coo_dxyCalculate abscissa and ordinate on a shape
coo_eccentricityboundingboxCalculates the eccentricity (bounding box) of a shape
coo_eccentricityeigenCalculates the eccentricity (using eigenvalues) of a shape
coo_elongationCalculates the elongation of a shape
coo_extractExtract coordinates from a shape
coo_flipFlips shapes
coo_force2closeForces shapes to close
coo_interpolateInterpolates coordinates
coo_jitterJitters shapes
coo_ldkDefines landmarks interactively
coo_leftRetains coordinates with negative x-coordinates
coo_lengthCalculates the length of a shape
coo_listpanelPlots sets of shapes.
coo_lolliPlots (lollipop) differences between two configurations
coo_lwCalculates length and width of a shape
coo_nbCounts coordinates
coo_oscilloMomocs' 'oscilloscope' for Fourier-based approaches
coo_perimCalculates the perimeter
coo_perimcumCalculates the cumulative chordal distance along a shape.
coo_perimptsCalculates the chordal distance along a shape.
coo_plotPlots a single shape
coo_rectangularityCalculates the rectangularity of a shape
coo_rectilinearityCalculates the rectilinearity of a shape
coo_revReverses coordinates
coo_rightRetains coordinates with positive x-coordinates
coo_rotateRotates coordinates
coo_rotatecenterRotates shapes with a custom center
coo_rubanPlots differences as (colored) segments aka a ruban
coo_sampleSample coordinates (among points)
coo_samplerrSamples coordinates (regular radius)
coo_scaleScales coordinates
coo_scalexyShrinks coordinates in one direction
coo_shearShears shapes
coo_sliceSlices shapes between successive coordinates
coo_slideSlides coordinates
coo_slidedirectionSlides coordinates in a particular direction
coo_slidegapSlides coordinates using the widest gap
coo_smoothSmoothes coordinates
coo_smoothcurveSmoothes coordinates on curves
coo_solidityCalculates the solidity of a shape
coo_tangleCalculates the tangent angle along the perimeter of a shape
coo_template'Templates' shapes
coo_theta3Calculate the angle formed by three (x; y) coordinates
coo_thetaptsCalculates the angle of every edge of a shape
coo_transTranslates coordinates
coo_trimTrims both ends coordinates from shape
coo_trimbottomTrims bottom coordinates from shape
coo_trimtopTrims top coordinates from shape
coo_upRetains coordinates with positive y-coordinates
coo_widthCalculates the width of a shape
cpx2cooConverts complex to cartesian coordinates
dA wrapper to calculates euclidean distances between two...
d2mConverts a data.frame of coordinates to a matrix of...
data_apodemusData: Outline coordinates of Apodemus (wood mouse) mandibles
data_botData: Outline coordinates of beer and whisky bottles.
data_chaffData: Landmark and semilandmark coordinates on cereal glumes
data_charringData: Outline coordinates from an experimental charring on...
data_flowerData: Measurement of iris flowers
data_heartsData: Outline coordinates of hand-drawn hearts
data_molarsData: Outline coordinates of 360 molars
data_mosquitoData: Outline coordinates of mosquito wings.
data_mouseData: Outline coordinates of mouse molars
data_nsfishesData: Outline coordinates of North Sea fishes
data_oakData: Configuration of landmarks of oak leaves
data_oleaData: Outline coordinates of olive seeds open outlines.
data_shapesData: Outline coordinates of various shapes
data_triloData: Outline coordinates of cephalic outlines of trilobite
data_wingsData: Landmarks coordinates of mosquito wings
def_ldkDefines new landmarks on Out and Opn objects
def_linksDefines links between landmarks
def_slidingsDefines sliding landmarks matrix
dfourierDiscrete cosinus transform
dfourier_iInveste discrete cosinus transform
dfourier_shapeCalculates and draws 'dfourier' shapes
dissolveDissolves Coe objects
edCalculates euclidean distance between two points.
ediCalculates euclidean intermediate between two points.
edmCalculates euclidean distance every pairs of points in two...
edm_nearestCalculates the shortest euclidean distance found for every...
efourierElliptical Fourier transform
efourier_iInverse elliptical Fourier transform
efourier_normNormalizes harmonic coefficients.
efourier_shapeCalculates and draw 'efourier' shapes.
exportExports Coe objects and shapes
fgProcrustesFull Generalized Procrustes alignment between shapes
fgsProcrustesFull Generalized Procrustes alignment between shapes with...
filterFilters (ala dplyr) on Momocs objects
flip_PCaxesFlips PCA axes
fProcrustesFull Procrustes alignment between two shapes
get_chull_areaCalculates convex hull area/volume of PCA scores
get_ldkRetrieves landmarks coordinates
get_pairsGet paired individual on a Coe, PCA or LDA objects
get_slidingsExtracts sliding landmarks coordinates
harm.contribHarmonic contribution to shape
harm_powCalculates harmonic power given a list from e/t/rfourier
hist.OutCoeHistogram of morphometric coefficients
img_plotPlots a .jpg image
import_ConteExtracts outlines coordinates from an image silhouette
import_jpgExtracts outline coordinates from multiple .jpg files
import_jpg1Extracts outline coordinates from a single .jpg file
import_StereoMorphImports files creates by StereoMorph into Momocs
import_tpsImports a tps file
import_txtImports coordinates from a .txt file
isVarious class/component testers
is_clockwiseTests if shapes are developping clockwise or anticlockwise
is_closedTests if shapes are closed
is_equallyspacedradiiTests if coordinates likely have equally spaced radii
KMEANSKMEANS on PCA objects
l2aConverts a list of coordinates to an array of coordinates
l2mConverts a list of coordinates to a matrix of coordinates.
LDALinear Discriminant Analysis on Coe objects
LdkBuilds an Ldk object
ldk_checkChecks 'ldk' shapes
ldk_chullDraws convex hulls around landmark positions
ldk_confellDraws confidence ellipses for landmark positions
ldk_contourDraws kernel density contours around landmark
ldk_labelsAdd landmarks labels
ldk_linksDraws links between landmarks
lf_structureExtracts structure from filenames
links_allCreates links (all pariwise combinations) between landmarks
links_delaunayCreates links (Delaunay triangulation) between landmarks
list_classesList available methods for any object and other classes for a...
m2aConverts a matrix of coordinates to an array of coordinates
m2dConverts a matrix of coordinates to a two-columns data.frame
m2lConverts a matrix of coordinates to a list of coordinates.
m2llConverts a matrix of coordinates into a list of matrices
MANOVAMultivariate analysis of (co)variance on Coe objects
MANOVA_PWPairwise Multivariate analyses of variance
measureMeasures shape descriptors
MomocsMomocs
Momocs_helpBrowse Momocs online doc
Momocs_versionInstall and load the last version of Momocs
mshapesMean shape calculation for Coo, Coe, etc.
mutateMutates (ala dplyr) on Momocs objects
nef2CoeImports .nef to Coe objects
npolyCalculate natural polynomial fits on open outlines
NtablePlots confusion matrix of sample sizes within $fac
ntsrow2CooImports .nts to Coo objects
OpnBuilds an Opn object
OpnCoeBuilds an OpnCoe object
opolyCalculate orthogonal polynomial fits on open outlines
OutBuilds an Out object
OutCoeBuilds an OutCoe object
panel2Family picture of shapes (ggplot2)
panel.CooFamily picture of shapes
PCAPrincipal component analysis on Coe objects
PCcontribShape variation along PC axes
permPermutes and breed Coe (and others) objects
pix2chcConverts (x; y) coordinates to chaincoded coordinates
plot2.PCAPlots Principal Component Analysis ala ggplot2
plot3.PCA#' @describeIn plot.PCA #' @export mplot <- plot.PCA Plots a...
plot.CooGraphical inspection of shapes
plot_CVPlots a cross-validation table as an heatmap
plot_CV2Plots a cross-correlation table
plot_devsegmentsDraws colored segments from a matrix of coordinates.
plot.LDAPlots Linear Discriminant Analysis
plot_mshapesPairwise comparison of a list of shapes
plot.PCAPlots Principal Component Analysis
poly_iCalculates shape from a polynomial model
pos.shapesCalculates nice positions on a plane for drawing shapes
pProcrustesPartial Procrustes alignment between two shapes
PtolemyPtolemaic ellipses and illustration of efourier
rearrange_ldkRearrange, (select and reorder) landmarks to retain
reexportsObjects exported from other packages
reLDA"Redo" a LDA on new data
renameRenames (ala dplyr) on Momocs objects
rePCA"Redo" a PCA on a new Coe
rescaleRescale coordinates from pixels to real length units
rfourierRadii variation Fourier transform (equally spaced radii)
rfourier_iInverse radii variation Fourier transform
rfourier_shapeCalculates and draw 'rfourier' shapes.
rm_asymRemoves asymmetric and symmetric variation on OutCoe objects
rm_harmRemoves harmonics from Coe objects
rm_uncompleteRemoves shapes with incomplete slices
rw_facRenames levels on Momocs objects
sample_fracSamples a fraction of shapes in Momocs objects
sample_nSamples n shapes on Momocs objects
screeMethods for PCA eigen values
selectSelects (ala dplyr) on Momocs objects
sfourierRadii variation Fourier transform (equally spaced curvilinear...
sfourier_iInverse radii variation Fourier transform
sfourier_shapeCalculates and draw 'sfourier' shapes.
sliceSlices (ala dplyr) on Momocs objects
slidings_schemeExtracts partitions of sliding coordinates
stack2Family picture of shapes (ggplot2)
stack.CooFamily picture of shapes
subsetSubsets on Momocs objects
symmetryCalcuates symmetry indices on OutCoe objects
tableCross-tabulates objects
tfourierTangent angle Fourier transform
tfourier_iInverse tangent angle Fourier transform
tfourier_shapeCalculates and draws 'tfourier' shapes.
tie_jpg_txtBinds .jpg outlines from .txt landmarks taken on them
tps2cooReads a single tps-like shape as lines
tps2dThin Plate Splines for 2D data
tps_arrDeformation 'vector field' using Thin Plate Splines
tps_gridDeformation grids using Thin Plate Splines
tps_isoDeformation isolines using Thin Plate Splines.
tps_rawVanilla Thin Plate Splines
TraCoeTraditional morphometrics class
trussTruss measurement
validateValidates Coo objects
vecs_paramSome vector utilities.
which_outIdentify outliers
vbonhomme/Momocs documentation built on Dec. 5, 2017, 9:29 p.m.