rm_by_trajnum: Remove subjects by trajectory number

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

Remove subjects by trajectory number

Description

Specify a minimum number of trajectories that each subject must complete during a treatment, trial, or session.

Usage

rm_by_trajnum(
  obj_name,
  trajnum = 5,
  mirrored = FALSE,
  treatment1,
  treatment2,
  ...
)

Arguments

obj_name	The input viewr object; a tibble or data.frame with attribute pathviewr_steps that includes "viewr". Trajectories must be predefined (i.e. via separate_trajectories()).
trajnum	Minimum number of trajectories; must be numeric.
mirrored	Does the data have mirrored treatments? If so, arguments treatment1 and treatment2 must also be provided, indicating the names of two mirrored treatments, both of which must meet the trajectory threshold specified in trajnum. Default is FALSE.
treatment1	The first treatment or session during which the threshold must be met.
treatment2	A second treatment or session during which the threshold must be met.
...	Additional arguments passed to/from other pathviewr functions.

Details

Depending on analysis needs, users may want to remove subjects that have not completed a certain number of trajectories during a treatment, trial, or session. If mirrored = FALSE, no treatment information is necessary and subjects will be removed based on total number of trajectories as specified in trajnum. If mirrored = TRUE, the treatment1 and treatment2 parameters will allow users to define during which treatments or sessions subjects must reach threshold as specified in the trajnum argument. For example, if mirrored = TRUE, setting treatment1 = "latA", treatment2 = "latB" and trajnum = 5 will remove subjects that have fewer than 5 trajectories during the "latA" treatment AND the "latB" treatment. treatment1 and treatment2 should be levels within a column named "treatment".

Value

A viewr object; a tibble or data.frame with attribute pathviewr_steps that includes "viewr" that now has fewer observations (rows) as a result of removal of subjects with too few trajectories according to the trajnum parameter.

Author(s)

Melissa S. Armstrong

Examples

library(pathviewr)

## 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, isolate, and label trajectories
motive_full <-
  motive_data %>%
  clean_viewr(desired_percent = 50,
              max_frame_gap = "autodetect",
              span = 0.95)

##Remove subjects that have not completed at least 150 trajectories:
motive_rm_unmirrored <-
  motive_full %>%
  rm_by_trajnum(trajnum = 150)

## Add treatment information
motive_full$treatment <- c(rep("latA", 100),
                           rep("latB", 100),
                           rep("latA", 100),
                           rep("latB", 149))

## Remove subjects by that have not completed at least 10 trajectories in
## both treatments
motive_rm_mirrored <-
  motive_full %>%
  rm_by_trajnum(
    trajnum = 10,
    mirrored = TRUE,
    treatment1 = "latA",
    treatment2 = "latB"
  )

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