insert_treatments: Inserts treatment and experiment information

In pathviewr: Wrangle, Analyze, and Visualize Animal Movement Data

Inserts treatment and experiment information

Description

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

Usage

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.

Details

All length measurements reported in meters.

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

Author(s)

Eric R. Press

See Also

Other utility functions: clean_by_span(), remove_duplicate_frames(), remove_vel_anomalies(), set_traj_frametime()

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)

 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)


## 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)
names(flydra_box)

pathviewr documentation built on March 31, 2023, 5:47 p.m.