Filter (clean) MiteMap result — filter

This function filter MiteMap data according to several parameters. It removes: the first seconds of each run, runs with aberrant range of x or y values, points with aberrant x or y values, runs with a total time superior to maximum_time. It can also center the x and y values by additioning a constant to all x and y values. By default the center of the arena is located at (0,0) with a diameter of 40mm.

Usage

filter_mitemap(
  MiteMap,
  first_seconds_to_delete = 2,
  bad_range_value_x = 42,
  bad_range_value_y = 42,
  max_x_value = 21,
  min_x_value = -21,
  max_y_value = 21,
  min_y_value = -21,
  maximum_time = 302,
  center_x = 0,
  center_y = 0,
  verbose = TRUE
)

Arguments

MiteMap: (required) The result of import_mitemap ($resulting_data) for raw_data
first_seconds_to_delete: (default: 2) How many seconds to delete?
bad_range_value_x: (default: 45) The range value of x that is superior to what we expect. This param filter values on the File_name basis.
bad_range_value_y: (default: 45) The range value of y that is superior to what we expect. This param filter values on the File_name basis.
max_x_value: (default: 21) Maximum value for x axis. This param filter values on the time-point (one line) basis.
min_x_value: (default: -21) Minimum value for x axis. This param filter values on the time-point (one line) basis.
max_y_value: (default: 21) Maximum value for y axis. This param filter values on the time-point (one line) basis.
min_y_value: (default: -21) Minimum value for y axis. This param filter values on the time-point (one line) basis.
maximum_time: (default: 603) The final value of time (in seconds)). This param filter values on the File_name basis.
center_x: (int, default 0) Center the value of x by additioning center_x mm to x.mm.
center_y: (int, default 0) Center the value of y by additioning center_y mm to y.mm.
verbose: (Logical, default = TRUE) If TRUE, the function print additional information.

Value

a filtered tibble

Details

The order of filtering is:

Remove runs (filename) with a total time superior to 'maximum_time'.
Remove the first 'first_seconds_to_delete' seconds of each run.
Remove runs (filename) with aberrant range of x or y values (i.e. superior to 'bad_range_value_x' or 'bad_range_value_y').
Remove points with aberrant x or y values (i.e. x.mm. < 'min_x_value' or x.mm. > 'max_x_value', y.mm. < 'min_y value' or y.mm. > 'max_y_value').
Center the x and y values by additioning 'center_x' and 'center_y' to all x and y values.

Author

Adrien Taudière

Examples

mm_csv <- import_mitemap(
  system.file("extdata", "mitemap_example", package = "MiteMapTools"),
  file_name_column = "File (mite ID)", verbose = FALSE, clean = FALSE
)
dim(mm_csv)
#> [1] 76032    35

MM_filtered_1 <- filter_mitemap(mm_csv)
#> Rows removed when clearing for run with times sup to maximum_time: 0 (0 runs)
#> Rows removed when clearing the first secondes: 603
#> Rows removed when clearing bad x range: 2798 (2 runs)
#> Rows removed when clearing bad y range: 0 (0 runs)
#> Rows removed when clearing bad x values: 1960
#> Rows removed when clearing bad y values: 26
#> 
#> Total rows after filtering: 70828 (from 76032)
#> Total runs after filtering: 50 (from 53)
dim(MM_filtered_1)
#> [1] 70828    35

MM_filtered_2 <- filter_mitemap(mm_csv,
  bad_range_value_x = 41,
  bad_range_value_y = 44,
  first_seconds_to_delete = 1,
  maximum_time = 301.1
)
#> Rows removed when clearing for run with times sup to maximum_time: 12941 (9 runs)
#> Rows removed when clearing the first secondes: 359
#> Rows removed when clearing bad x range: 2798 (2 runs)
#> Rows removed when clearing bad y range: 0 (0 runs)
#> Rows removed when clearing bad x values: 1960
#> Rows removed when clearing bad y values: 26
#> 
#> Total rows after filtering: 58177 (from 76032)
#> Total runs after filtering: 41 (from 53)
dim(MM_filtered_2)
#> [1] 58177    35