Adds information about treatment and experimental set up to viewr objects for analysis in other pathviewr functions

insert_treatments(
  obj_name,
  tunnel_config = "box",
  perch_2_vertex = NULL,
  vertex_angle = NULL,
  tunnel_width = NULL,
  tunnel_length = NULL,
  stim_param_lat_pos = NULL,
  stim_param_lat_neg = NULL,
  stim_param_end_pos = NULL,
  stim_param_end_neg = NULL,
  treatment = NULL
)

Arguments

obj_name

The input viewr object; a tibble or data.frame with attribute pathviewr_steps that includes "viewr"

tunnel_config

The configuration of the experimental tunnel. Currently, pathviewr supports rectangular "box" and V-shaped tunnel configurations.

perch_2_vertex

If using a V-shaped tunnel, this is the vertical distance between the vertex and the height of the perches. If the tunnel does not have perches, insert the vertical distance between the vertex and the height of the origin (0,0,0).

vertex_angle

If using a V-shaped tunnel, the angle of the vertex (in degrees) vertex_angle defaults to 90.

tunnel_width

If using a box-shaped tunnel, the width of the tunnel.

tunnel_length

The length of the tunnel.

stim_param_lat_pos

The size of the stimulus on the lateral positive wall of the tunnel. Eg. for 10cm wide gratings, stim_param_lat_pos = 0.1.

stim_param_lat_neg

The size of the stimulus on the lateral negative wall of the tunnel..

stim_param_end_pos

The size of the stimulus on the end positive wall of the tunnel.

stim_param_end_neg

The size of the stimulus on the end negative wall of the tunnel.

treatment

The name of the treatment assigned to all rows of the viewr object. Currently only able to accept a single treatment per viewr data object.

Value

A viewr object (tibble or data.frame with attribute pathviewr_steps that includes "treatments added"). Depending on the argument tunnel_config, the viewr object also includes columns storing the values of the supplied arguments. This experimental information is also stored in the viewr object's metadata

Details

All length measurements reported in meters.

See also

Author

Eric R. Press

Examples

## Import sample data from package motive_data <- read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv", package = 'pathviewr')) flydra_data <- read_flydra_mat(system.file("extdata", "pathviewr_flydra_example_data.mat", package = 'pathviewr'), subject_name = "birdie_sanders") ## Clean data up to and including get_full_trajectories() motive_data_full <- motive_data %>% relabel_viewr_axes() %>% gather_tunnel_data() %>% trim_tunnel_outliers() %>% rotate_tunnel() %>% select_x_percent(desired_percent = 50) %>% separate_trajectories(max_frame_gap = "autodetect") %>% get_full_trajectories(span = 0.95)
#> autodetect is an experimental feature -- please report issues.
flydra_data_full <- flydra_data %>% redefine_tunnel_center(length_method = "middle", height_method = "user-defined", height_zero = 1.44) %>% select_x_percent(desired_percent = 50) %>% separate_trajectories(max_frame_gap = "autodetect") %>% get_full_trajectories(span = 0.95)
#> autodetect is an experimental feature -- please report issues.
## Now add information about the experimental configuration. In this example, ## a V-shaped tunnel in which the vertex is 90deg and lies 0.40m below the ## origin. The visual stimuli on the lateral and end walls have a cycle ## length of 0.1m and 0.3m respectively, and the treatment is labeled ## "lat10_end30" motive_v <- motive_data_full %>% insert_treatments(tunnel_config = "v", perch_2_vertex = 0.4, vertex_angle = 90, tunnel_length = 2, stim_param_lat_pos = 0.1, stim_param_lat_neg = 0.1, stim_param_end_pos = 0.3, stim_param_end_neg = 0.3, treatment = "lat10_end_30") # For an experiment using the box-shaped configuration where the tunnel is 1m # wide and 3m long and the visual stimuli on the lateral and end walls have a # cycle length of 0.2 and 0.3m, respectively, and the treatment is labeled # "lat20_end30". flydra_box <- flydra_data_full %>% insert_treatments(tunnel_config = "box", tunnel_width = 1, tunnel_length = 3, stim_param_lat_pos = 0.2, stim_param_lat_neg = 0.2, stim_param_end_pos = 0.3, stim_param_end_neg = 0.3, treatment = "lat20_end30") ## Check out the new columns in the resulting objects names(motive_v)
#> [1] "tunnel_config" "perch_2_vertex" "vertex_angle" #> [4] "tunnel_length" "stim_param_lat_pos" "stim_param_lat_neg" #> [7] "stim_param_end_pos" "stim_param_end_neg" "treatment" #> [10] "frame" "time_sec" "subject" #> [13] "position_length" "position_width" "position_height" #> [16] "rotation_length" "rotation_width" "rotation_height" #> [19] "rotation_real" "mean_marker_error" "traj_id" #> [22] "file_sub_traj" "traj_length" "start_length" #> [25] "end_length" "length_diff" "start_length_sign" #> [28] "end_length_sign" "direction"
names(flydra_box)
#> [1] "tunnel_config" "tunnel_width" "tunnel_length" #> [4] "stim_param_lat_pos" "stim_param_lat_neg" "stim_param_end_pos" #> [7] "stim_param_end_neg" "treatment" "frame" #> [10] "time_sec" "subject" "position_length" #> [13] "position_width" "position_height" "velocity" #> [16] "length_inst_vel" "width_inst_vel" "height_inst_vel" #> [19] "traj_id" "file_sub_traj" "traj_length" #> [22] "start_length" "end_length" "length_diff" #> [25] "start_length_sign" "end_length_sign" "direction"