# Wrangle, Analyze, and Visualize Animal Movement Data

## Documentation for package ‘pathviewr’ version 1.1.8

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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