PupilPre {PupilPre}

PupilPre: Preprocessing Pupil Size Data.

Description

The PupilPre package provides a set of functions for preparing pupil size data collected with SR Research Eyelink eye trackers.

Processing functions

• The function ppl_prep_data returns a data table with correctly assigned classes for important columns.

• The function ppl_select_recorded_eye returns a data table with data from the the recorded eye in new columns (IA_ID and IA_LABEL).

• The function recode_off_screen recodes samples with NA if gaze coordinates indicate that the sample was taken while the pupil was off-screen.

• The function ppl_rm_extra_DVcols removes DataViewer coumns that are not necessary for preprocessing with this package.

• The function clean_blink returns a data table for which blinks have been removed based on the parameters provided.

• The function clean_artifact returns a data table for which artifacts have been removed based on the parameters provided.

• The function apply_cleanup_change applies user-selected changes to the automatic cleanup.

• The function apply_user_cleanup returns a data table for which the manually selected artifacts have been removed.

• The function rm_sparse_events removes events that do not contain enough data in the baseline and/or critical windows, as specified by the user.

• The function interpolate_NAs returns a data table in which NAs have been replaced using linear interpolation.

• The function apply_butter applies a Butterworth filter to the pupil size data.

• The function trim_filtered removes a specified number of milliseconds from the beginning and the end of each filtered event, as to remove artifacts created by the filter.

• The function downsample returns a data table for which the data have been downsampled using the specified sampling rate.

• The function baseline returns a data table for which the pupil data have been baselined using the specified method.

Utility functions

• The function ppl_check_eye_recording returns a summary of whether or not the dataset contains gaze data in both the Right and Left interest area columns.

• The function blink_summary returns a summary of Eyelink marked blinks by Event, Subject, or Item.

• The function NA_summary returns a summary of missing data by Event, Subject, or Item.

• The function check_baseline examines the data within a specified baseline window.

• The function compare_summary returns a summary of comparison between the columns Pupil and Pupil_Previous.

Plotting functions

• The function ppl_plot_avg returns a plot of the grand or conditional averages of pupil dilation along with error bars.

• The function ppl_plot_avg_contour returns a contour plot of the conditional average of pupil dilation over Time and a specified continuous variable.

• The function ppl_plot_avg_cdiff returns a plot of the average difference between two conditions for pupil dilation with error bars.

• The function plot_events returns image files containing plots for each event by a group and saves into a specified directory.

Interactive functions

• The function user_cleanup_app opens a Shiny app for identifying and marking datapoints associated with artifacts.

• The function plot_summary_app opens a Shiny app for inspecting by-subject or by-item averages within a specified time window.

• The function plot_compare_app opens a Shiny app for inspecting events for comparing the current pupil column to the previous pupil column.

• The function verify_cleanup_app plots the data points changed during the previously completed auto cleanup, allowing the user to reject the cleanup for specific events.

• The function butter_filter_app produces a plot of filtered pupil data over the original data to visually inspect the effect of different filter settings.

Notes

• The vignettes are available via browseVignettes(package = "PupilPre").

• A list of all available functions is provided in help(package = "PupilPre").

• This package can be cited using the information obtained from citation("PupilPre") or print(citation("PupilPre"), bibtex = TRUE)

Author(s)

Aki-Juhani Kyröläinen, Vincent Porretta, Jacolien van Rij, Juhani Järvikivi

Maintainer: Aki-Juhani Kyröläinen, ([e-mail])

McMaster University, Canada