Wrangle, Analyze, and Visualize Animal Movement Data

[Up] [Top]

Documentation for package ‘pathviewr’ version 1.1.7

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