redefine_tunnel_center: "Center" the tunnel data, i.e. translation but no rotation

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

"Center" the tunnel data, i.e. translation but no rotation

Description

Redefine the center (0, 0, 0,) of the tunnel data via translating positions along axes.

Usage

redefine_tunnel_center(
  obj_name,
  axes = c("position_length", "position_width", "position_height"),
  length_method = c("original", "middle", "median", "user-defined"),
  width_method = c("original", "middle", "median", "user-defined"),
  height_method = c("original", "middle", "median", "user-defined"),
  length_zero = NA,
  width_zero = NA,
  height_zero = NA,
  ...
)

Arguments

obj_name	The input viewr object; a tibble or data.frame with attribute pathviewr_steps that includes "viewr"
axes	Names of axes to be centered
length_method	Method for length
width_method	Method for width
height_method	Method for height
length_zero	User-defined value
width_zero	User-defined value
height_zero	User-defined value
...	Additional arguments passed to/from other pathviewr functions

Details

For each _method argument, there are four choices of how centering is handled: 1) "original" keeps axis as is – this is how width and (possibly) height should be handled for flydra data; 2) "middle" is the middle of the range of data: (min + max) / 2; 3) "median" is the median value of data on that axis. Probably not recommended; and 4) "user-defined" lets the user customize where the (0, 0, 0) point in the tunnel will end up. Each _zero argument is subtracted from its corresponding axis' data.

Value

A viewr object (tibble or data.frame with attribute pathviewr_steps that includes "viewr") in which data have been translated according to the user's inputs, generally with (0, 0, 0,) being relocated to the center of the tunnel.

Author(s)

Vikram B. Baliga

See Also

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

Other tunnel standardization functions: rotate_tunnel(), standardize_tunnel()

Examples

## Import the Flydra example data included in
## the package
flydra_data <-
  read_flydra_mat(
    system.file("extdata",
                "pathviewr_flydra_example_data.mat",
                package = 'pathviewr'),
    subject_name = "birdie_wooster"
  )

## Re-center the Flydra data set.
## Width will be untouched
## Length will use the "middle" definition
## And height will be user-defined to be
## zeroed at 1.44 on the original axis
flydra_centered <-
  flydra_data %>%
  redefine_tunnel_center(length_method = "middle",
                         height_method = "user-defined",
                         height_zero = 1.44)

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