Man pages for vbonhomme/Momocs
Morphometrics using R

add_ldkAdds new landmarks on Out and Opn objects
andnowAnd now, what to do?
arrangeArrange rows by variables
as_dfTurn Momocs objects into tydy data_frames
at_leastRetain groups with at least n shapes
babelConvert (x; y) coordinates to chaincoded coordinates
bezierCalculates Bezier coefficients from a shape
bezier_iCalculates a shape from Bezier coefficients
boxplot.OutCoeBoxplot of morphometric coefficients
boxplot.PCABoxplot on PCA objects
breedJitters Coe (and others) objects
bridgesConvert between different classes
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
chopSplit to several objects based on a factor
classification_metricsCalculate classification metrics on a confusion matrix
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
color_transparencyTransparency helpers and palettes
combineCombine several objects
complexConvert complex to/from cartesian coordinates
CooCoo "super" class
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_angle_edgesCalculates the angle of every edge of a shape
coo_angle_tangentCalculates the tangent angle along the perimeter of a shape
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 (recursive) convex hull of a shape
coo_circularityCalculates the Haralick's 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_eccentricityCalculates the eccentricity 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_intersect_angleNearest intersection between a shape and a segment specified...
coo_intersect_segmentNearest intersection between a shape and a segment
coo_is_closedTest if shapes are closed
coo_jitterJitters shapes
coo_ldkDefines landmarks interactively
coo_leftRetains coordinates with negative x-coordinates
coo_lengthCalculates the length of a shape
coo_likely_clockwiseTests if shapes are (likely) developping clockwise or...
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 perimeter and variations
coo_plotPlots a single shape
coo_rangeCalculate coordinates range
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_sample_propSample a proportion of coordinates (among points)
coo_samplerrSamples coordinates (regular radius)
coo_scalarsCalculates all scalar descriptors of shape
coo_scaleScales coordinates
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_tacCalculates the total absolute curvature of a shape
coo_template'Templates' shapes
coo_transTranslates coordinates
coo_trimTrims both ends coordinates from shape
coo_trimbottomTrims bottom coordinates from shape
coo_trimtopTrims top coordinates from shape
coo_trussTruss measurement
coo_untiltxRemoves rotation so that the centroid and a given point are...
coo_upRetains coordinates with positive y-coordinates
coo_widthCalculates the width of a shape
dA wrapper to calculates euclidean distances between two...
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_ldk_angleAdd new landmarks based on angular positions
def_ldk_tipsDefine tips as new landmarks
def_linksDefines links between landmarks
def_slidingsDefines sliding landmarks matrix
dfourierDiscrete cosinus transform
dfourier_iInveste discrete cosinus transform
dfourier_shapeCalculates and draws 'dfourier' shapes
dissolveDissolve Coe objects
drawersgrindr drawers for shape plots
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 (and its normalization)
efourier_iInverse elliptical Fourier transform
efourier_shapeCalculates and draw 'efourier' shapes.
exportExports Coe objects and shapes
fac_dispatcherBrew and serve fac from Momocs object
fgProcrustesFull Generalized Procrustes alignment between shapes
fgsProcrustesFull Generalized Procrustes alignment between shapes with...
filterSubset based on conditions
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
img_plotPlots a .jpg image
import_ConteExtract outlines coordinates from an image silhouette
import_jpgExtract outline coordinates from multiple .jpg files
import_jpg1Extract outline coordinates from a single .jpg file
import_StereoMorphImport files creates by StereoMorph into Momocs
import_tpsImport a tps file
import_txtImport coordinates from a .txt file
inspectGraphical inspection of shapes
isClass and component testers
is_equallyspacedradiiTests if coordinates likely have equally spaced radii
KMEANSKMEANS on PCA objects
KMEDOIDSKMEDOIDS
layersgrindr layers for multivariate plots
layers_morphospaceMorphospace layers
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_structurebind_db.Coe <- bind_db.Coo Extracts structure from filenames
links_allCreates links (all pairwise combinations) between landmarks
links_delaunayCreates links (Delaunay triangulation) between landmarks
MANOVAMultivariate analysis of (co)variance on Coe objects
MANOVA_PWPairwise Multivariate analyses of variance
MDS(Metric) multidimensional scaling
measureMeasures shape descriptors
MomocsMomocs
Momocs_helpersMomocs helpers
morphospace_positionsCalculates nice positions on a plane for drawing shapes
mosaicPlots mosaics of shapes.
MSHAPESMean shape calculation for Coo, Coe, etc.
mutateAdd new variables
NMDSNon metric multidimensional scaling
npolyCalculate natural polynomial fits on open outlines
OpnBuilds an Opn object
OpnCoeBuilds an OpnCoe object
opolyCalculate orthogonal polynomial fits on open outlines
OutBuilds an Out object
OutCoeBuilds an OutCoe object
palettesColor palettes
panel.CooFamily picture of shapes
papersgrindr papers for shape plots
PCAPrincipal component analysis on Coe objects
PCcontribShape variation along PC axes
permPermutes and breed Coe (and others) objects
pileGraphical pile 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_LDALDA plot using grindr layers
plot.LDAPlots Linear Discriminant Analysis
plot_MSHAPESPairwise comparison of a list of shapes
plot_NMDSNMDS plot unsing grindr layers
plot_PCAPCA plot using grindr layers
plot.PCAPlots Principal Component Analysis
plot_silhouetteSilhouette plot
plot_tablePlots confusion matrix of sample sizes within $fac
poly_iCalculates shape from a polynomial model
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
renameRename columns by name
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_missingRemove shapes with missing data in fac
rm_uncompleteRemove shapes with incomplete slices
rw_facRenames levels on Momocs objects
sample_fracSample a fraction of shapes
sample_nSample n shapes
screeHow many axes to retain this much of variance or trace ?
selectSelect columns by name
sfourierRadii variation Fourier transform (equally spaced curvilinear...
sfourier_iInverse radii variation Fourier transform
sfourier_shapeCalculates and draw 'sfourier' shapes.
sliceSubset based on positions
slidings_schemeExtracts partitions of sliding coordinates
stack.CooFamily picture of shapes
subsetSubsetize various Momocs objects
symmetryCalcuates symmetry indices on OutCoe 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
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
verifyValidates Coo objects
which_outIdentify outliers
vbonhomme/Momocs documentation built on Oct. 30, 2018, 10:23 p.m.