separate_trajectories: Separate rows of data into separately labeled trajectories.

In vbaliga/pathviewR: Wrangle, Analyze, and Visualize Animal Movement Data

Separate rows of data into separately labeled trajectories.

Description

Separate rows of data into separately labeled trajectories.

Usage

separate_trajectories(
  obj_name,
  max_frame_gap = 1,
  frame_rate_proportion = 0.1,
  frame_gap_messaging = FALSE,
  frame_gap_plotting = FALSE,
  ...
)

Arguments

obj_name	The input viewr object; a tibble or data.frame with attribute pathviewr_steps that includes "viewr"
max_frame_gap	Default 1; defines the largest permissible gap in data before a new trajectory is forced to be defined. Can be either a numeric value or "autodetect". See Details for more.
frame_rate_proportion	Default 0.10; if max_frame_gap = "autodetect", proportion of frame rate to be used as a reference (see Details).
frame_gap_messaging	Default FALSE; should frame gaps be reported in the console?
frame_gap_plotting	Default FALSE; should frame gap diagnostic plots be shown?
...	Additional arguments passed to/from other pathviewr functions

Details

This function is designed to separate rows of data into separately labeled trajectories.

The max_frame_gap parameter determines how trajectories will be separated. If numeric, the function uses the supplied value as the largest permissible gap in frames before a new trajectory is defined.

If max_frame_gap = "autodetect" is used, the function attempts to guesstimate the best value(s) of max_frame_gap. This is performed separately for each subject in the data set, i.e. as many max_frame_gap values will be estimated as there are unique subjects. The highest possible value of any max_frame_gap is first set as a proportion of the capture frame rate, as defined by the frame_rate_proportion parameter (default 0.10). For each subject, a plot of total trajectory counts vs. max frame gap values is created internally (but can be plotted via setting frame_gap_plotting = TRUE). As larger max frame gaps are allowed, trajectory count will necessarily decrease but may reach a value that likely represents the "best" option. The "elbow" of that plot is then used to find an estimate of the best max frame gap value to use.

Value

A viewr object (tibble or data.frame with attribute pathviewr_steps that includes "viewr") in which a new column file_sub_traj is added, which labels trajectories within the data by concatenating file name, subject name, and a trajectory number (all separated by underscores).

Author(s)

Vikram B. Baliga and Melissa S. Armstrong

See Also

Other data cleaning functions: gather_tunnel_data(), get_full_trajectories(), quick_separate_trajectories(), redefine_tunnel_center(), relabel_viewr_axes(), rename_viewr_characters(), rotate_tunnel(), select_x_percent(), standardize_tunnel(), trim_tunnel_outliers(), visualize_frame_gap_choice()

Other functions that define or clean trajectories: get_full_trajectories(), quick_separate_trajectories(), visualize_frame_gap_choice()

Examples

## Import the example Motive data included in the package
motive_data <-
  read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
                              package = 'pathviewr'))

## Clean the file. It is generally recommended to clean up to the
## "select" step before running select_x_percent().
motive_selected <-
  motive_data %>%
  relabel_viewr_axes() %>%
  gather_tunnel_data() %>%
  trim_tunnel_outliers() %>%
  rotate_tunnel() %>%
  select_x_percent(desired_percent = 50)

## Now separate trajectories using autodetect
motive_separated <-
  motive_selected %>%
  separate_trajectories(max_frame_gap = "autodetect",
                        frame_rate_proportion = 0.1)

## See new column file_sub_traj for trajectory labeling
names(motive_separated)

vbaliga/pathviewR documentation built on March 16, 2023, 4:13 p.m.