Function reference • pathviewr

Data import functions Functions for creating ‘viewr’ objects from external data
`read_motive_csv()`	Import data from a CSV exported from Optitrack's Motive software
`read_flydra_mat()`	Import data from a MAT file exported from Flydra software
`as_viewr()`	Convert data from another format into a viewr object
Utility functions Functions for wrangling and cleaning ‘viewr’ objects
`get_header_viewr()`	Extract header info from imported viewr object
`relabel_viewr_axes()`	Relabel the dimensions as length, width, and height
`gather_tunnel_data()`	Gather data columns into key-value pairs
`rescale_tunnel_data()`	Rescale position data within a `viewr` object
`rename_viewr_characters()`	Rename subjects in the data via pattern detection
`trim_tunnel_outliers()`	Trim out artifacts and other outliers from the extremes of the tunnel
`rotate_tunnel()`	Rotate a tunnel so that perches are approximately aligned
`standardize_tunnel()`	Rotate and center a tunnel based on landmarks
`redefine_tunnel_center()`	"Center" the tunnel data, i.e. translation but no rotation
`select_x_percent()`	Select a region of interest within the tunnel
`quick_separate_trajectories()`	Quick version of separate_trajectories()
`separate_trajectories()`	Separate rows of data into separately labeled trajectories.
`get_full_trajectories()`	Retain trajectories that span a selected region of interest
`section_tunnel_by()`	Bin data along a specified axis
`exclude_by_velocity()`	Remove trajectories entirely, based on velocity thresholds
`fill_traj_gaps()`	Interpolate gaps within trajectories
`rm_by_trajnum()`	Remove subjects by trajectory number
`insert_treatments()`	Inserts treatment and experiment information
`set_traj_frametime()`	Redefine frames and time stamps on a per-trajectory basis
`clean_by_span()`	Remove file_sub_traj entries that do not span the full region of interest
`remove_duplicate_frames()`	Remove any duplicates or aliased frames within trajectories
`remove_vel_anomalies()`	Remove any rows which show sharp shifts in velocity that are likely due to tracking errors
Analytical functions Functions for quantitative analysis
`find_curve_elbow()`	Find the "elbow" of a curve.
`get_velocity()`	Get instantaneous velocity for subjects
`get_traj_velocities()`	Recompute trajectory-specific velocities
`calc_min_dist_box()`	Calculate minimum distance to lateral and end walls in a box-shaped experimental tunnel
`calc_min_dist_v()`	Calculate minimum distance to lateral and end walls in a V-shaped experimental tunnel
`get_vis_angle()`	Estimate visual angles from a subject's perspective in an experimental tunnel
`get_sf()`	Estimate the spatial frequency of visual stimuli from the subject's perspective in an experimental tunnel.
`get_dist_point_line()`	Compute distance between a point and a line
`get_3d_cross_prod()`	Compute the cross product of two 3D vectors
`rad_2_deg()`	Convert radians to degrees
`deg_2_rad()`	Convert degrees to radians
`get_2d_angle()`	Compute an angle in 2D space
`get_3d_angle()`	Compute an angle in 3D space
Plotting functions Functions for plotting ‘viewr’ objects
`visualize_frame_gap_choice()`	Visualize the consequence of using various max_frame_gap values
`plot_viewr_trajectories()`	Plot each trajectory within a viewr object
`plot_by_subject()`	Plot trajectories and density plots of position by subject
All-in-one functions Complete data import and cleaning pipelines
`clean_viewr()`	All-in-one function to clean imported objects
`import_and_clean_viewr()`	Import + clean_viewr()
Batch analysis functions Functions for the analysis of multiple files or `viewr` objects
`import_batch()`	Batch import of files for either Motive or Flydra (but not a mix of both)
`clean_viewr_batch()`	Batch clean viewr files
`import_and_clean_batch()`	Batch import and clean files
`bind_viewr_objects()`	Bind viewr objects

Reference

Data import functions

Utility functions

Analytical functions

Plotting functions

All-in-one functions

Batch analysis functions