Package index
Main functions
Main functions for estimating kinematic parameters from midline data. These are more or less in the order you would use them. Functions ending in _df
operate on a data frame and often add multiple columns to the data frame. The data frame should have two identifier columns:
-
frame
: Identifies instants in time -
point
: Identifies locations along the body, so that they can be ordered from head to tail.
To use identifier columns with different names, the functions take options .frame
and .point
. To change the names of the output columns, the functions use an option .out
. .out
can be a vector containing the names of the columns, or a named list.
-
arclength()
- Calculate arc length along a 2D curve
-
interpolate_points_df()
- Interpolates and smooths a 2D curve at new arc length
-
interpolate_width()
- Interpolates and scales fish body width
-
get_midline_center_df()
- Gets the center of a midline for many midlines in a data frame
-
get_primary_swimming_axis_df()
- Gets the primary swimming axis for many midlines
-
curvature()
- Estimates curvature for a single curve
-
hilbert_phase()
- Compute phase of an oscillation using the Hilbert transform
-
peak_phase()
- Compute phase of an oscillation by locating peaks and zero crossings.
-
get_frequency()
- Estimates the cycle frequency based on time and phase
-
get_wavelength()
- Computes the body wavelength based on the phase at each point and the arc length
-
get_body_cycle_numbers_df()
- Gets oscillation cycle numbers for a midline data set
-
apply_filter()
- Apply a filter constructed with build_filter
-
build_filter()
- Constructs a smoothing filter
-
check.out()
- Helper function to check the
.out
and.out_default
variables used in this package
-
check_if_overwrite_columns()
- Check if a data frame has columns that we might overwrite
-
deriv()
- Estimate first or second derivatives for dy/dx.
-
get_cycle_numbers()
- Gets cycle numbers from a phase variable
-
get_primary_swimming_axis()
- Gets the main swimming axis from a midline
-
get_volume()
- Gets the volume of segments of a cylindrical body with elliptical cross section
-
interpolate_peak_location()
- Interpolate the location of a peak based on three points
-
interpolate_points_frame()
- Interpolates x and y points on a curve to different arc lengths
-
pivot_kinematics_longer()
- Pivots a kinematics dataset into long format
-
skip_na()
- Skip NAs when running a function on a vector