Package index

Morphometric methods

Outlines

eft(): Elliptic Fourier Transform
eft_i(): Inverse elliptic Fourier transform
eft_name(): Name elliptic Fourier coefficients
eft_norm(): Normalize elliptic Fourier coefficients
eft_split(): Split EFT coefficient vector into components

Curves

opoly(): Orthogonal Polynomial Transform
opoly_i(): Inverse orthogonal polynomial transform
opoly_name(): Name orthogonal polynomial coefficients
npoly(): Natural Polynomial Transform
npoly_i(): Inverse natural polynomial transform
npoly_name(): Name natural polynomial coefficients
dct(): Discrete Cosine Transform
dct_i(): Inverse discrete cosine transform
dct_name(): Name discrete cosine transform coefficients
dct_split(): Split DCT coefficient vector into components

Classes and printers

Mostly cosmetics

as_coo() as_out() as_ldk() as_xy() as_ldk_id() as_cur() as_path() as_meas() as_coe() as_eft() as_rft() as_dct() as_npoly() as_opoly() as_proc(): Coerce to Momocs morphometric classes

Dispatcher and function factories

Exposed extending helpers

make_coo_function(): Create a coo function with automatic dispatch
make_get_function(): Create a get function with automatic dispatch
get_coo_cols() get_all_coo_cols(): Identify coo columns in a tibble
get_coe_cols() get_all_coe_cols(): Identify coe columns in a tibble

Verbs

ease common operations

fold(): Fold multiple columns into a single list-column
unfold(): Unfold a list-column into multiple columns or a matrix
wrap(): Wrap coordinates from rows to list-column of matrices
unwrap(): Unwrap coordinates from list-column of matrices to rows
front(): Relocate morphometric columns to front
declass(): Remove Momocs classes

Dataset

To play with

bot: Bottles dataset
hearts: Heart dataset
olea: Olea dataset
wings: Wings dataset
shapes: Shapes dataset

coo_* coordinate transformations

Functions that take coo and return coo

Basic transformations

coo_center(): Center coordinates
coo_translate(): Translate coordinates
coo_scale(): Scale to unit centroid size

Rotation

coo_rotate(): Rotate coordinates
coo_rotate_around(): Rotate around a center point
coo_untilt_x() coo_untilt_y(): Untilt to axis

Alignment

Align shapes using internal information

coo_align(): Align shape to principal axes
coo_align_minor(): Align shape to minor and major axes (swapped)
coo_align_calliper() coo_align_minradius(): Align to special features

Baseline registration

Align shapes using landmarks

coo_baseline() coo_bookstein(): Baseline correction (Bookstein registration)

Sampling and smoothing

Sample up and down coordinates number

coo_sample() coo_sample_prop(): Sample coordinates
coo_sample_regular_radius(): Sample at regular angles from centroid
coo_smooth() coo_smooth_fixed(): Smooth coordinates

Slide

Change row ordering

coo_slide_id() coo_slide_ldk() coo_slide_closest() coo_slide_angle() coo_slide_direction() coo_slide_gap(): Slide coordinates along outline

Direction

Control trigonometric or clockwise direction

coo_reverse(): Reverse point order
coo_direction_positive() coo_direction_negative(): Ensure positive (counter-clockwise) direction

Open/close shapes

coo_close() coo_open(): Close or open outlines
coo_close_spread(): Close outline by spreading gap

Template shapes

Standardize on bounding boxes

coo_template() coo_template_relatively(): Template shapes to standard size

Flipping

Reflect shapes

coo_flip_x() coo_flip_xaxis() coo_flip_y() coo_flip_yaxis(): Flip coordinates

Filtering

Extract coordinates based on spatial criteria

coo_extract() coo_head() coo_tail(): Extract or subset coordinates
coo_trim_head() coo_trim_tail() coo_trim_both(): Trim points from outline ends
coo_up() coo_down() coo_right() coo_left(): Filter points by direction from centroid

Translate variants

coo_translate_jitter(): Jitter coordinates
coo_translate_to_xaxis(): Translate shape to x-axis
coo_translate_to_yaxis(): Translate shape to y-axis

Cut and join

Cut single shapes into several and back

get_cut(): Cut outline at landmarks
get_join(): Join curves into closed outline

Misc operations

Where to put them? Why not here?

coo_check(): Check and clean coordinates
coo_shear_x() coo_shear_y(): Shear coordinates

get_* shape descriptors

Functions that take coo and return scalar descriptors

Measurement helper

Compute and add multiple measurements

measure(): Measure shape properties
available_measures(): List available measurements

Basic size measures

get_area(): Get area of a closed outline
get_perim() get_perim_along() get_perim_cum(): Get perimeter measurements

Other size measures

Overall size and dimensions

get_length(): Get length
get_width(): Get width
get_calliper() get_calliper_ids(): Get calliper
get_centroid_size() centsize(): Get centroid size
get_centroid_size_norm() centsize_norm(): Get normalized centroid size

Circularity and aspect

get_elongation(): Get elongation
get_circularity() get_circularity_norm() get_circularity_haralick(): Get circularity measures

Shape complexity

get_convexity(): Get convexity
get_solidity(): Get solidity
get_rugosity(): Get rugosity
get_compactness(): Get compactness
get_rectangularity(): Get rectangularity
get_rectilinearity(): Get rectilinearity

get_* other operations

Functions that take coo and return other than coo and scalars

Landmarks

ldk_id coordinates extraction

get_ldk(): Extract landmark coordinates

Transformations

Extract and apply geometric transformations

get_transform(): Extract transformation between two configurations
get_transformed(): Apply transformation to coordinates

get_centroid(): Get centroid of a shape
get_centroid_distance(): Get distances from centroid

Distances and angles

Distances and angular measures

get_centroid_distance(): Get distances from centroid
get_perim() get_perim_along() get_perim_cum(): Get perimeter measurements
get_lw(): Get length and width
get_calliper() get_calliper_ids(): Get calliper
get_truss(): Get truss (all pairwise distances)

Angles

get_angles(): Get angles from centroid
get_angle_edges(): Get angles at vertices
get_angle_tangent(): Get tangent angles

Extents and boundaries

get_range(): Get coordinate ranges
get_range_diff(): Get range span
get_bbox(): Get bounding box corners
get_coords_nb(): Get number of coordinates

Direction and position

Orientation and point location

get_direction_sign(): Get outline direction sign
get_closest() get_closest_angle(): Find closest point to target
get_closest_direction(): Get point closest to a given direction

Convex hull

Convex hull extraction and analysis

get_chull() get_chull_id(): Get convex hull
get_chull_onion(): Get convex hull layers (onion peeling)

Visualization

Plotting and display functions

pile(): Plot shapes stacked together
mosaic(): Plot shapes in grid mosaic layout
p() draw_landmarks() draw_landmarks_as_numbers() draw_outlines() draw_centroid() draw_first_point() draw_links(): Minimal plotting system for morphometric shapes

Reimport

From other packages

pipes %>% %T>% %$%: Pipe operators