A B C D E F G H I K L M N O P R S T V W
Momocs-package | Momocs |
a2l | Converts an array of coordinates to a list of matrices |
a2m | Converts an array of coordinates to a matrix |
add_ldk | Adds new landmarks on Out and Opn objects |
apodemus | Data: Outline coordinates of Apodemus (wood mouse) mandibles |
arrange | Arranges (ala dplyr) on Momocs objects |
as.Out | Convert an OutCoe object into an Out object |
as.PCA | Principal component analysis on Coe objects |
as_df | Converts Momocs objects to data.frames |
at_least | Retains group with at least a certain number of individuals |
bezier | Calculates Bezier coefficients from a shape |
bezier_i | Calculates a shape from Bezier coefficients |
bind_db | Binds with a database |
bot | Data: Outline coordinates of beer and whisky bottles. |
boxplot.Coe | Boxplot of morphometric coefficients |
boxplot.OutCoe | Boxplot of morphometric coefficients |
boxplot.PCA | Boxplot on PCA objects |
breed | Jitters Coe (and others) objects |
breed.Coe | Jitters Coe (and others) objects |
breed.default | Jitters Coe (and others) objects |
calibrate_deviations | Quantitative calibration, through deviations, for Out and Opn objects |
calibrate_harmonicpower | Quantitative calibration, through harmonic power, for Out and Opn objects |
calibrate_r2 | Quantitative r2 calibration for Opn objects |
calibrate_reconstructions | Calibrate using reconstructed shapes |
chaff | Data: Landmark and semilandmark coordinates on cereal glumes |
charring | Data: Outline coordinates from an experimental charring on cereal grains |
chc2Out | Converts chain-coded coordinates to Out object |
chc2pix | Converts chain-coded coordinates to (x; y) coordinates |
chop | Chops (rough slicing) Momocs objects |
classification_metrics | Calculate classification metrics on a confusion matrix |
classify | Classify using LDA |
CLUST | Hierarchical clustering |
CLUST.default | 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 vector. |
coeff_split | Converts a numerical description of harmonic coefficients to a named list. |
col_alpha | Transparency helpers and palettes |
col_autumn | Some color palettes |
col_black | Some color palettes |
col_bw | Some color palettes |
col_cold | Some color palettes |
col_gallus | Some color palettes |
col_grey | Some color palettes |
col_heat | Some color palettes |
col_hot | Some color palettes |
col_india | Some color palettes |
col_qual | Some color palettes |
col_sari | Some color palettes |
col_solarized | Some color palettes |
col_spring | Some color palettes |
col_summer | Some color palettes |
col_summer2 | Some color palettes |
col_transp | Transparency helpers and palettes |
combine | Combines Momocs objects |
conf_ell | Confidence ellipses |
Coo | Coo "super" class |
coo2cpx | Converts cartesian to complex 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_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_centre | Centers coordinates |
coo_centsize | Calculates centroid size |
coo_check | Checks shapes |
coo_chull | Calculates the convex hull of a shape |
coo_chull_onion | Peeling points by recursively removing their convex hulls |
coo_circularity | Calculates the circularity of a shape |
coo_circularityharalick | Calculates the Haralick's circularity of a shape |
coo_circularitynorm | Calculates the 'normalized' circularity of a shape |
coo_close | Closes/uncloses shapes |
coo_compactness | Calculates the circularity of a shape |
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_eccentricityboundingbox | Calculates the eccentricity (bounding box) of a shape |
coo_eccentricityeigen | Calculates the eccentricity (using eigenvalues) of a shape |
coo_elongation | Calculates the elongation of a shape |
coo_extract | Extract coordinates from a shape |
coo_flipx | Flips shapes |
coo_flipy | Flips shapes |
coo_force2close | Forces shapes to close |
coo_interpolate | Interpolates coordinates |
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_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 the perimeter |
coo_perimcum | Calculates the cumulative chordal distance along a shape. |
coo_perimpts | Calculates the chordal distance along a shape. |
coo_plot | Plots a single shape |
coo_plot.default | Plots a single shape |
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_samplerr | Samples coordinates (regular radius) |
coo_scale | Scales coordinates |
coo_scalex | Shrinks coordinates in one direction |
coo_scaley | Shrinks coordinates in one direction |
coo_shapefactor | Calculates the circularity of a shape |
coo_shearx | Shears shapes |
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_tangle | Calculates the tangent angle along the perimeter of a shape |
coo_template | 'Templates' shapes |
coo_theta3 | Calculate the angle formed by three (x; y) coordinates |
coo_thetapts | Calculates the angle of every edge of a shape |
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_unclose | Closes/uncloses shapes |
coo_up | Retains coordinates with positive y-coordinates |
coo_width | Calculates the width of a shape |
cpx2coo | Converts complex to cartesian coordinates |
d | A wrapper to calculates euclidean distances between two points |
d2m | Converts a data.frame of coordinates to a matrix of coordinates. |
def_ldk | Defines new landmarks on Out and Opn objects |
def_links | Defines links between landmarks |
def_slidings | Defines sliding landmarks matrix |
dfourier | Discrete cosinus transform |
dfourier.Coo | Discrete cosinus transform |
dfourier.default | Discrete cosinus transform |
dfourier.Opn | Discrete cosinus transform |
dfourier_i | Investe discrete cosinus transform |
dfourier_shape | Calculates and draws 'dfourier' shapes |
dissolve | Dissolves Coe objects |
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 | Elliptical Fourier transform |
efourier.default | Elliptical Fourier transform |
efourier.Out | Elliptical Fourier transform |
efourier_i | Inverse elliptical Fourier transform |
efourier_norm | Normalizes harmonic coefficients. |
efourier_shape | Calculates and draw 'efourier' shapes. |
export | Exports Coe objects and shapes |
fgProcrustes | Full Generalized Procrustes alignment between shapes |
fgsProcrustes | Full Generalized Procrustes alignment between shapes with sliding landmarks |
filter | Filters (ala dplyr) on Momocs objects |
flip_PCaxes | Flips PCA axes |
flower | Data: Measurement of iris flowers |
fProcrustes | Full Procrustes alignment between two shapes |
get_chull_area | Calculates convex hull area/volume of PCA scores |
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 |
harm_pow | Calculates harmonic power given a list from e/t/rfourier |
hcontrib | Harmonic contribution to shape |
hcontrib.OutCoe | Harmonic contribution to shape |
hearts | Data: Outline coordinates of hand-drawn hearts |
hist.Coe | Histogram of morphometric coefficients |
hist.OutCoe | Histogram of morphometric coefficients |
img_plot | Plots a .jpg image |
img_plot0 | Plots a .jpg image |
import_Conte | Extracts outlines coordinates from an image silhouette |
import_jpg | Extracts outline coordinates from multiple .jpg files |
import_jpg1 | Extracts outline coordinates from a single .jpg file |
import_StereoMorph_curve | Imports files creates by StereoMorph into Momocs |
import_StereoMorph_curve1 | Imports files creates by StereoMorph into Momocs |
import_StereoMorph_ldk | Imports files creates by StereoMorph into Momocs |
import_StereoMorph_ldk1 | Imports files creates by StereoMorph into Momocs |
import_tps | Imports a tps file |
import_txt | Imports coordinates from a .txt file |
is | Various class/component testers |
is_anticlockwise | Tests if shapes are developping clockwise or anticlockwise |
is_clockwise | Tests if shapes are developping clockwise or anticlockwise |
is_closed | Tests if shapes are closed |
is_Coe | Various class/component testers |
is_Coo | Various class/component testers |
is_equallyspacedradii | Tests if coordinates likely have equally spaced radii |
is_fac | Various class/component testers |
is_LDA | Various class/component testers |
is_Ldk | Various class/component testers |
is_ldk | Various class/component testers |
is_LdkCoe | Various class/component testers |
is_links | Various class/component testers |
is_open | Tests if shapes are closed |
is_Opn | Various class/component testers |
is_OpnCoe | Various class/component testers |
is_Out | Various class/component testers |
is_OutCoe | Various class/component testers |
is_PCA | Various class/component testers |
is_shp | Various class/component testers |
is_slidings | Various class/component testers |
is_TraCoe | Various class/component testers |
KMEANS | KMEANS on PCA objects |
KMEANS.PCA | KMEANS on PCA objects |
l2a | Converts a list of coordinates to an array of coordinates |
l2m | Converts a list of coordinates to a matrix of coordinates. |
LDA | Linear Discriminant Analysis on Coe objects |
LDA.default | Linear Discriminant Analysis on Coe objects |
LDA.PCA | 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 |
ldk_plot | Plots a single shape |
lf_structure | Extracts structure from filenames |
links_all | Creates links (all pariwise combinations) between landmarks |
links_delaunay | Creates links (Delaunay triangulation) between landmarks |
list_classes_for_this_method | List available methods for any object and other classes for a method |
list_methods_for_this_class | List available methods for any object and other classes for a method |
m2a | Converts a matrix of coordinates to an array of coordinates |
m2d | Converts a matrix of coordinates to a two-columns data.frame |
m2l | Converts a matrix of coordinates to a list of coordinates. |
m2ll | Converts a matrix of coordinates into a list of matrices |
MANOVA | Multivariate analysis of (co)variance on Coe objects |
MANOVA.OpnCoe | Multivariate analysis of (co)variance on Coe objects |
MANOVA.OutCoe | Multivariate analysis of (co)variance on Coe objects |
MANOVA.PCA | Multivariate analysis of (co)variance on Coe objects |
MANOVA_PW | Pairwise Multivariate analyses of variance |
MANOVA_PW.PCA | Pairwise Multivariate analyses of variance |
measure | Measures shape descriptors |
molars | Data: Outline coordinates of 360 molars |
Momocs | Momocs |
Momocs_currentCRANversion | Install and load the last version of Momocs |
Momocs_currentGitHubversion | Install and load the last version of Momocs |
Momocs_help | Browse Momocs online doc |
Momocs_lastversion | Install and load the last version of Momocs |
Momocs_version | Install and load the last version of Momocs |
mosquito | Data: Outline coordinates of mosquito wings. |
mouse | Data: Outline coordinates of mouse molars |
MSHAPES | Mean shape calculation for Coo, Coe, etc. |
mshapes | Mean shape calculation for Coo, Coe, etc. |
mshapes.array | Mean shape calculation for Coo, Coe, etc. |
mshapes.Ldk | Mean shape calculation for Coo, Coe, etc. |
mshapes.LdkCoe | Mean shape calculation for Coo, Coe, etc. |
mshapes.list | Mean shape calculation for Coo, Coe, etc. |
mshapes.OpnCoe | Mean shape calculation for Coo, Coe, etc. |
mshapes.OutCoe | Mean shape calculation for Coo, Coe, etc. |
mshapes.PCA | Mean shape calculation for Coo, Coe, etc. |
mutate | Mutates (ala dplyr) on Momocs objects |
nef2Coe | Imports .nef to Coe objects |
npoly | Calculate natural polynomial fits on open outlines |
npoly.default | Calculate natural polynomial fits on open outlines |
npoly.Opn | Calculate natural polynomial fits on open outlines |
npoly_i | Calculates shape from a polynomial model |
nsfishes | Data: Outline coordinates of North Sea fishes |
Ntable | Plots confusion matrix of sample sizes within $fac |
ntscol2Coo | Imports .nts to Coo objects |
ntsrow2Coo | Imports .nts to Coo objects |
oak | Data: Configuration of landmarks of oak leaves |
olea | Data: Outline coordinates of olive seeds open outlines. |
Opn | Builds an Opn object |
OpnCoe | Builds an OpnCoe object |
opoly | Calculate orthogonal polynomial fits on open outlines |
opoly.default | Calculate orthogonal polynomial fits on open outlines |
opoly.Opn | Calculate orthogonal polynomial fits on open outlines |
opoly_i | Calculates shape from a polynomial model |
Out | Builds an Out object |
OutCoe | Builds an OutCoe object |
Palettes | Some color palettes |
panel | Family picture of shapes |
panel.Coo | Family picture of shapes |
panel.Ldk | Family picture of shapes |
panel.Opn | Family picture of shapes |
panel.Out | Family picture of shapes |
panel.OutCoe | Family picture of shapes |
panel2 | Family picture of shapes (ggplot2) |
PCA | Principal component analysis on Coe objects |
PCA.default | Principal component analysis on Coe objects |
PCA.LdkCoe | Principal component analysis on Coe objects |
PCA.OpnCoe | Principal component analysis on Coe objects |
PCA.OutCoe | Principal component analysis on Coe objects |
PCA.TraCoe | Principal component analysis on Coe objects |
PCcontrib | Shape variation along PC axes |
PCcontrib.PCA | Shape variation along PC axes |
perm | Permutes and breed Coe (and others) objects |
perm.Coe | Permutes and breed Coe (and others) objects |
perm.default | Permutes and breed Coe (and others) objects |
pix2chc | Converts (x; y) coordinates to chaincoded coordinates |
plot.Coo | Graphical inspection of shapes |
plot.LDA | Plots Linear Discriminant Analysis |
plot.PCA | Plots Principal Component Analysis |
plot2 | Plots Principal Component Analysis ala ggplot2 |
plot2.PCA | Plots Principal Component Analysis ala ggplot2 |
plot3 | #' @describeIn plot.PCA #' @export mplot <- plot.PCA Plots a combination of the three first PCs |
plot3.PCA | #' @describeIn plot.PCA #' @export mplot <- plot.PCA Plots a combination of the three first PCs |
plot_CV | Plots a cross-validation table as an heatmap |
plot_CV.default | Plots a cross-validation table as an heatmap |
plot_CV.LDA | Plots a cross-validation table as an heatmap |
plot_CV2 | Plots a cross-correlation table |
plot_CV2.LDA | Plots a cross-correlation table |
plot_CV2.table | Plots a cross-correlation table |
plot_devsegments | Draws colored segments from a matrix of coordinates. |
plot_mshapes | Pairwise comparison of a list of shapes |
pos.shapes | Calculates nice positions on a plane for drawing shapes |
pProcrustes | Partial Procrustes alignment between two shapes |
Ptolemy | Ptolemaic ellipses and illustration of efourier |
rearrange_ldk | Rearrange, (select and reorder) landmarks to retain |
reLDA | "Redo" a LDA on new data |
reLDA.Coe | "Redo" a LDA on new data |
reLDA.default | "Redo" a LDA on new data |
reLDA.PCA | "Redo" a LDA on new data |
rename | Renames (ala dplyr) on Momocs objects |
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.default | Radii variation Fourier transform (equally spaced radii) |
rfourier.Out | 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_asym.default | Removes asymmetric and symmetric variation on OutCoe objects |
rm_asym.OutCoe | Removes asymmetric and symmetric variation on OutCoe objects |
rm_harm | Removes harmonics from Coe objects |
rm_sym | Removes asymmetric and symmetric variation on OutCoe objects |
rm_sym.default | Removes asymmetric and symmetric variation on OutCoe objects |
rm_sym.OutCoe | Removes asymmetric and symmetric variation on OutCoe objects |
rm_uncomplete | Removes shapes with incomplete slices |
rw_fac | Renames levels on Momocs objects |
rw_rule | Renames levels on Momocs objects |
sample_frac | Samples a fraction of shapes in Momocs objects |
sample_n | Samples n shapes on Momocs objects |
scree | Methods for PCA eigen values |
scree.LDA | Methods for PCA eigen values |
scree.PCA | Methods for PCA eigen values |
scree_min | Methods for PCA eigen values |
scree_plot | Methods for PCA eigen values |
select | Selects (ala dplyr) on Momocs objects |
sfourier | Radii variation Fourier transform (equally spaced curvilinear abscissa) |
sfourier.default | Radii variation Fourier transform (equally spaced curvilinear abscissa) |
sfourier.Out | Radii variation Fourier transform (equally spaced curvilinear abscissa) |
sfourier_i | Inverse radii variation Fourier transform |
sfourier_shape | Calculates and draw 'sfourier' shapes. |
shapes | Data: Outline coordinates of various shapes |
slice | Slices (ala dplyr) on Momocs objects |
slidings_scheme | Extracts partitions of sliding coordinates |
stack.Coo | Family picture of shapes |
stack.Ldk | Family picture of shapes |
stack2 | Family picture of shapes (ggplot2) |
subset.Coe | Subsets on Momocs objects |
subset.Coo | Subsets on Momocs objects |
subset.PCA | Subsets on Momocs objects |
symmetry | Calcuates symmetry indices on OutCoe objects |
table | Cross-tabulates objects |
table.Coe | Cross-tabulates objects |
table.Coo | Cross-tabulates objects |
table.default | Cross-tabulates objects |
table.LDA | Cross-tabulates objects |
table.PCA | Cross-tabulates objects |
tfourier | Tangent angle Fourier transform |
tfourier.default | Tangent angle Fourier transform |
tfourier.Out | 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 |
tps2coo | Reads a single tps-like shape as lines |
tps2d | Thin Plate Splines for 2D data |
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 |
TraCoe | Traditional morphometrics class |
trilo | Data: Outline coordinates of cephalic outlines of trilobite |
truss | Truss measurement |
validate | Validates Coo objects |
vecs_param | Some vector utilities. |
which_out | Identify outliers |
wings | Data: Landmarks coordinates of mosquito wings |